Autoimmune Protocol Diet

Diet Reference Archive: an elimination diet promoted for autoimmune conditions

Autoimmune Protocol Diet

A strict version of the paleo diet that removes many food groups for a period and then brings them back one at a time. It is promoted to people with autoimmune conditions to ease symptoms and find foods they react to.

Family: Therapeutic and elimination dietsPromoted by: patient-led online communities, the books of Sarah Ballantyne and Mickey Trescott, and a practitioner training programFirst appeared: online communities from about 2011; first complete book in 2014GRADE: Very low for observed clinical remission by 11 weeks during an AIP program added to usual medical care, adults with active Crohn’s disease or ulcerative colitis, from 1 study with no concurrent comparison group, so the remission cannot be attributed to the program (Konijeti et al., 2017); this page’s own judgment

ON THIS PAGE

1. In brief
2. Overview
3. In practice
4. For the coach
5. The evidence (opens on request)
6. Mechanisms (opens on request)
7. Risks, contraindications and myths (opens on request)
8. Key terms
9. Review questions
10. References
11. Evidence rating and review record

The summary and sections 1 to 3 are the short version and are open when the page loads. Sections 4 to 6 hold the research detail, the biology, and the cautions. Each of those opens when you select its heading, and you can read the page without opening them. This page covers one named diet. The general method of removing foods and bringing them back is on the Elimination Diets page, the eating pattern this diet builds on is on the Paleo Diet page, and celiac disease is on the Gluten-Free Diet page; this page does not repeat their evidence. Back to the Diet Reference Archive index.

In brief

What is it? The autoimmune protocol, usually called AIP, is a strict version of the paleo diet. For a set period a person removes grains, legumes, dairy, eggs, nuts, seeds, nightshade vegetables such as tomatoes and potatoes, coffee, alcohol, added sugars and food additives, and eats meat, fish, vegetables and fruit. Then the removed foods come back one at a time, to see which ones seem to bring symptoms back (Konijeti et al., 2017; Trescott, n.d.-a).

Does it work? No randomized trial of the diet was found in the searches for this page. A handful of small studies, each following one group of about 9 to 28 people for 8 to 12 weeks without a concurrent comparison group, reported fewer symptoms and better quality of life in inflammatory bowel disease, Hashimoto’s thyroiditis and rheumatoid arthritis. Without a comparison group, those studies cannot show that the diet caused the change, and this page rates every one of those results very low in certainty. In the 2 thyroid studies, the main thyroid antibody did not fall (Abbott et al., 2019; Ihnatowicz et al., 2023).

The American College of Rheumatology’s guideline conditionally recommends against formally defined diets other than a Mediterranean-style diet for rheumatoid arthritis, a list that names paleo and elimination diets but not AIP itself (England et al., 2023).

Is it safe? In the small studies, most people had no serious problems, but some did. Two people with Crohn’s disease and narrowed sections of bowel got worse, and one was hospitalized for a partial blockage after eating much more raw vegetables (Konijeti et al., 2017). Because so many foods are removed, nutrients such as calcium and iodine need planning (National Institutes of Health Office of Dietary Supplements, 2024, 2026), and some people taking thyroid medication had their doses changed during a study (Abbott et al., 2019).

Who should not do it without talking to a doctor or dietitian first? Anyone using it for a diagnosed condition, because the condition’s treatment plan belongs with the physician and specialist. Most of all: people with Crohn’s disease, especially with a known narrowing of the bowel; people taking thyroid hormone, insulin, a sulfonylurea or warfarin; children and teenagers; people who are pregnant, breastfeeding or trying to conceive; people with kidney disease; anyone with a known food allergy; anyone with a current or past eating disorder; and vegetarians and vegans.

Related pages: Elimination Diets, Paleo Diet, Gluten-Free Diet and Anti-Inflammatory Diet. Full list on the archive index.

1. Overview

What you eat

During the elimination phase, meals are built from meat, poultry, fish and shellfish, organ meats such as liver, and a wide range of vegetables and fruit other than the nightshade family. Starchy roots such as sweet potatoes, cassava, taro and plantains take the place of grains. Fats come from olive oil, avocado, coconut and animal fats. Herbs and spices made from leaves, roots and bark, such as basil, thyme, ginger, garlic and turmeric, are used in place of seed and pepper spices. Fermented foods that contain no dairy, such as sauerkraut and kombucha, bone broth and sea vegetables such as nori are encouraged, and honey and maple syrup are allowed in moderation (Konijeti et al., 2017; Trescott, n.d.-a, 2026).

The plan has no calorie or portion targets; the rheumatoid arthritis study, for example, asked people to eat until satisfied (McNeill et al., 2026a). Promoters describe the aim as a diet dense in nutrients, and they pair it with attention to sleep, stress, physical activity and support from other people (Konijeti et al., 2017; Trescott, 2026).

What you avoid or limit

In the original version, now called Core AIP, which its main promoter says is the version used in all the published studies, these are removed completely for the elimination phase: all grains and pseudo-grains, including wheat, rice, corn, oats and quinoa; all dairy; eggs; all legumes, including peanuts, soy and green beans; nightshade vegetables and the spices made from them, including tomatoes, potatoes, peppers, eggplant and paprika; nuts and seeds and the spices, oils and foods made from them, including coffee and chocolate; processed vegetable oils; nonnutritive sweeteners; food additives such as emulsifiers and artificial colors; and alcohol (Trescott, n.d.-a). The inflammatory bowel disease study also asked people to avoid nonsteroidal anti-inflammatory drugs, a medicine question that belongs to the prescriber (Konijeti et al., 2017).

These are hard rules during elimination, not guidelines. In 2024 the promoter added a less strict Modified AIP that allows rice, pseudo-grains such as quinoa, legumes other than peanuts and soy, seeds and ghee; no published study has tested that version (Book Passage, n.d.; Trescott, n.d.-a).

Sources disagree about how long elimination lasts and what the phases are called. The main promoter recommends 30 to 90 days and describes 3 phases: a first phase of preparing before any food is removed, elimination and reintroduction (Trescott, n.d.-a, 2026). A 2025 review gives 6 weeks to 6 months and names the phases elimination, reintroduction and maintenance (Pardali et al., 2025), while a 2026 rheumatoid arthritis study gives 1 to 4 months (McNeill et al., 2026a). In the inflammatory bowel disease study, “maintenance” meant the opposite: 5 more weeks of holding the elimination diet before any food came back (Konijeti et al., 2017). When a client says “maintenance,” it is worth asking which one they mean.

Study versions differed too. The 2023 thyroid study used a version its researchers planned individually for each participant, and its authors describe the protocol as not precisely defined and without an exact template (Ihnatowicz et al., 2023).

Where it came from

The diet grew out of the paleo movement. A history published by the company of 2 of its earliest promoters dates its first threads to 2011, when people with autoimmune conditions who were following paleo diets came across the idea of an elimination diet aimed at autoimmunity through the work of several authors, including Loren Cordain. In 2012 Sarah Ballantyne, whom the researchers of a 2026 study describe as a biophysicist, began blogging guidance on elimination and reintroduction, and her book The Paleo Approach, published in 2014, became the protocol’s main guide. A cookbook by Mickey Trescott followed the same year (Autoimmune Wellness, n.d.). Those researchers, who studied the diet in rheumatoid arthritis, credit the original idea to Cordain and the detailed modern protocol to Ballantyne (McNeill et al., 2026a). The 2 accounts differ in emphasis rather than in substance.

The protocol spread first through blogs, cookbooks and online groups, and then into research. The same company history describes a gastroenterologist contacting its founders about a patient with inflammatory bowel disease, which led to the first study in 2016, and describes raising money for the later Hashimoto’s thyroiditis study (Autoimmune Wellness, n.d.). In 2017 Trescott, Ballantyne and Angie Alt started a training program for practitioners (AIP Certified Coach, n.d.). Ballantyne has since closed her website, The Paleo Mom, and moved to a different nutrition project; her closing page directs people looking for AIP information to the other promoters (Ballantyne, n.d.). In 2026 Trescott published The New Autoimmune Protocol, which presents the Core and Modified versions (Book Passage, n.d.).

What it claims to do

The main promoter calls AIP “an evidence-based framework” that helps people with autoimmune disease find which foods and lifestyle factors help or hinder their health, and says it is not a cure and not a replacement for medical care (Trescott, 2026). The same site says that removing common triggers and adding nutrient-dense foods reduces inflammation, supports the gut lining and improves immune regulation, and it reports that in one study “nearly half” of participants taking thyroid medication reduced their dose under medical supervision (Trescott, 2026). These are the promoter’s claims.

The underlying idea, as researchers describe it, is that certain food components may make the gut lining more permeable, often called “leaky gut,” so that food and bacterial fragments reach the immune system and drive autoimmune activity, and that removing those foods lets the gut and immune system settle (McNeill et al., 2026a; Pardali et al., 2025). Section 4 reports what the studies found, and section 5 says which parts of this idea have been shown in people.

What it gets right

AIP takes seriously how much autoimmune symptoms can affect daily life, and it puts vegetables, fruit, fish and minimally processed food at the center of the plate while removing added sugar and ultraprocessed foods. The American Heart Association lists eating plenty of vegetables and fruits, choosing minimally processed foods instead of ultraprocessed foods, and minimizing intake of added sugars among the features of a heart-healthy pattern (Lichtenstein et al., 2026). In the rheumatoid arthritis study, measured vegetable, fruit and fiber intakes rose and added sugar fell during the diet (McNeill et al., 2026a).

Its design also ends with reintroduction, which is meant to widen the diet rather than leave a long list of foods avoided for good, and its promoters describe it as working alongside medical care rather than in place of it (Trescott, 2026). The same heart association guidance lists whole grains as a feature of a heart-healthy pattern, which the elimination phase removes (Lichtenstein et al., 2026). These are the parts a coach can honor in a client’s reasons without endorsing the whole package.

How clients describe it, and what it gets confused with

Clients say “I’m doing AIP,” “I’m on the autoimmune paleo diet,” “I’ve cut out nightshades,” “I’m doing the elimination phase for my Hashimoto’s,” “I’m doing Modified AIP,” “my coach has me reintroducing egg yolks,” or “I’m healing my gut.” Each can mean something different: a short trial planned with a clinician, a long self-directed elimination, or a version a person has built from online lists. Asking who set it up, what condition it is for, and how long it is meant to last comes first. Clients may also have seen it in U.S. News’s diet profiles, where the AIP diet’s page, dated January 8, 2026, stated, when it was read for this page on October 21, 2026, that it is “not highly rated by experts in any category” (Jones, 2026); that is U.S. News’s rating.

It is most often confused with the Paleo Diet, which keeps eggs, nuts, seeds and nightshades; with the general clinical method on the Elimination Diets page, which a clinician uses to answer a specific question such as whether a food causes an allergic reaction; with the Gluten-Free Diet, which is the treatment for celiac disease; and with the broad label described on the Anti-Inflammatory Diet page. The Wahls diet for multiple sclerosis is a different modified paleo diet, described on the Paleo Diet page. “Healing my gut” can also point to Specific Carbohydrate Diet or GAPS Diet, which are separate topics on the archive index.

2. In practice

A typical day of eating

The day below is this page’s own illustration of the Core elimination phase, not a plan from a source. Breakfast might be a skillet of ground turkey with sweet potato, zucchini and spinach cooked in olive oil, with a cup of herbal tea. Lunch might be leftover roast chicken over greens with avocado, cucumber, olives and a dressing of olive oil and lemon, with an apple. Dinner might be baked salmon with roasted carrots and broccoli and mashed cassava or plantain, and a snack might be sauerkraut, coconut flakes or berries. Every packaged food is checked for grains, dairy, egg, soy, seed oils, pepper and additives, which is why most meals are cooked at home.

A person on Modified AIP could add rice, quinoa, lentils or white beans to the same meals (Trescott, n.d.-a). Calcium from the dairy that is gone, and iodine from the dairy, eggs and iodized salt a person may have used before, are what a dietitian is likely to check first; section 6 explains why.

Cost, products, and who profits

The diet itself is free, and many of its foods, such as vegetables, fruit, chicken and canned fish, are ordinary. Costs rise with specialty items, such as the coconut aminos, coconut milk and other coconut products on the main promoter’s food list (Trescott, n.d.-a) and the grass-fed or wild-caught animal proteins named in one review’s food list (Pardali et al., 2025). In the rheumatoid arthritis study, participants generally reported higher food costs at the start, mostly from buying compliant pantry staples, while some who usually ate out spent less (McNeill et al., 2026a), and in the follow-up interviews some described sourcing specialty items from several online suppliers (McNeill et al., 2026b). The searches for this page found no study that measured the cost of the diet in dollars.

Several businesses are built around the protocol. On November 8, 2026, one bookseller listed Trescott’s 2026 book The New Autoimmune Protocol at $35.00 (Book Passage, n.d.). The same day, the AIP Certified Coach training program, taught online by Trescott and Jaime Hartman, a National Board Certified Health and Wellness Coach, listed its fee for 2026 as $998 paid in full or $1,098 in 3 monthly payments, with a $35 yearly recertification fee, and said that completing it earns continuing education credits from the National Board for Health and Wellness Coaching, among others; enrollment showed a waitlist that day. The program says it is open to practitioners who already hold a certification or license to work with clients, that it is “for educational use only,” and that each graduate must assess their own legal scope of practice (AIP Certified Coach, n.d.). Those are the company’s statements.

Money and the promoters also run through the research. The Hashimoto’s study used the online coaching program of a company co-founded by one of its authors, Angie Alt, as its intervention; another author disclosed being paid $2,000 a year by that company as a medical advisor; the study was funded by $11,428.60 raised through crowdfunding; and a laboratory company supplied stool and organic acid tests (Abbott et al., 2019). The inflammatory bowel disease study used the same online program and thanked Trescott and Alt for their input (Konijeti et al., 2017). A funder’s or author’s interest does not by itself make a result wrong; section 4 says where it could have shaped one.

For someone with limited money, time or store access, the elimination phase is demanding, because it relies on cooking most meals from scratch. The less costly path runs through ordinary vegetables, fruit, frozen fish and inexpensive cuts of meat rather than specialty products, and any long-term plan for a diagnosed condition belongs with a dietitian. This is observation rather than measured data.

Environmental footprint

The searches for this page found no study of the environmental footprint of the autoimmune protocol. Like the paleo pattern it builds on, its elimination phase removes plant proteins and relies on meat, poultry and fish, so its footprint depends mostly on how much and what kind of animal food a person eats; the Paleo Diet page reports an estimate built from what U.S. adults with paleo-style diets reported eating, which is not a measurement of this diet.

Cultural fit

The foods removed include the staples of most food traditions: rice, wheat, corn, beans, lentils, soy, dairy, eggs, tomatoes, chilies, potatoes and most spices made from seeds and peppers, including cumin, coriander seed, mustard, black pepper and paprika. Cuisines built on rice and beans, tortillas and chilies, bread and cheese, lentils and seed spices, or tofu and soy sauce lose most of their foundation during elimination. Modified AIP restores rice and most legumes, which makes it easier to keep many traditional dishes (Trescott, n.d.-a).

For a vegetarian or vegan, the elimination phase removes many of their usual protein sources at once, and U.S. News said, when read on October 21, 2026, that it cannot be altered to accommodate a vegan diet (Jones, 2026). People who eat in a shared household, at work or at religious and family events will find the phase hardest there; section 3 covers what that means for coaching.

What makes people stop

Adherence was high in the studies, but they were short and heavily supported. In the inflammatory bowel disease study, 3 of the 18 people enrolled withdrew before it started because they could not commit to the diet, and at the end of the 6-week elimination phase 11 of the 15 who began had removed all the required foods (Chandrasekaran, Groven, et al., 2019; Konijeti et al., 2017). Both study teams credited intensive support from coaches, dietitians and an online group for adherence (Abbott et al., 2019; Konijeti et al., 2017).

The rheumatoid arthritis study interviewed its 9 participants after the diet and again a year later. During the diet, some described meals as bland, missed spicy food, and felt “diet fatigue” near the end, and eating out needed careful planning. Within a few weeks of the study ending, most had moved away from strict AIP, describing the mental effort and planning it took, and found the step-by-step reintroduction burdensome; only 1 person kept strict AIP for 3.5 months before reintroducing foods as the protocol describes (McNeill et al., 2026b). Beyond these studies, what follows is observation: travel, social meals and family events are where the diet is hardest to keep.

What happens when you stop

The searches for this page did not identify a study that followed people for 12 months on the diet itself. The longest follow-up found was the rheumatoid arthritis study’s interviews a year after an 8-week diet. Most participants had reintroduced foods without the structured process, some reported that symptoms came back after particular foods, 2 of them after nightshades, particularly potatoes, many foods were tolerated, and most described eating more healthily than before the study but more flexibly than AIP (McNeill et al., 2026b). That is what people reported, not a measured result; the study team says its 1-year measurements will be reported separately, and the searches for this page did not find them (McNeill et al., 2026a).

An online survey of 78 people with inflammatory bowel disease who used AIP found that people began reintroducing foods at very different times, from within 4 weeks to more than a year after starting; 13 percent had waited more than 12 months (Lee et al., 2019). A long, unplanned stay in elimination is one of the concerns raised in section 6.

Common variations

Core AIP is the original, fully restricted version used in the published studies; Modified AIP, introduced in 2024, allows rice, pseudo-grains, most legumes, seeds and ghee during elimination (Trescott, n.d.-a). People also follow versions they assemble themselves from online lists, which the main promoter says are often outdated or overly restrictive (Trescott, 2026). The Paleo Diet is the less restrictive parent pattern, and the Wahls diet for multiple sclerosis, a different modified paleo diet, is described there. The Elimination Diets page covers the clinical method, and the Low-FODMAP Diet and Whole30 are other named diets that remove foods and bring them back.

3. For the coach

SCOPE OF PRACTICE

A health and wellness coach does not prescribe, adjust, endorse or discourage the autoimmune protocol or any other way of eating, and does not diagnose or treat. The coach helps the client understand what they have chosen, notice how it is going, and decide what to do next. This diet is promoted for diagnosed medical conditions, so most of it sits on the clinical side of the line. Diagnosis and treatment of an autoimmune condition belong to the physician and the specialist, such as a gastroenterologist, endocrinologist or rheumatologist, and any plan to use the diet alongside that treatment belongs with them and a registered dietitian. A coach never suggests the protocol to treat a condition or as a way to find out what a client reacts to.

Clinical oversight applies to anyone using the diet for a diagnosed or suspected condition. The following groups need particular attention, with the appropriate clinician and dietitian involved:

• Symptoms that no clinician has evaluated: the client’s physician first, before any food is removed, including testing for celiac disease before gluten is removed.
• Crohn’s disease or another bowel condition, above all with a known stricture, a narrowing of the bowel: the gastroenterologist and a dietitian, before raw vegetables and fiber are increased.
• Taking levothyroxine or another thyroid hormone medicine: the client contacts the prescriber before a substantial change in eating. The prescriber decides what monitoring is needed and reviews changes in supplements, including calcium, and their timing. The coach does not order or interpret thyroid tests or change medication.
• Taking insulin or a sulfonylurea, or warfarin: the client keeps the prescriber informed before a substantial change in eating.
• Taking medicine for the autoimmune condition, such as steroids, mesalamine or a biologic: no change without the prescriber.
• Kidney disease: the kidney care team, because needs depend on stage, lab results and dialysis.
• A known food allergy: the allergist, who decides whether and how any food that has caused a reaction comes back.
• A child or teenager, or a person who is pregnant, breastfeeding or trying to conceive: the pediatric or obstetric clinician and a registered dietitian.
• A current or past eating disorder or disordered eating: the client’s clinician, through the coach’s own referral process or an existing care plan.
• A vegetarian or vegan: a registered dietitian, because the elimination phase removes many of the foods they use for protein.

The AIP Certified Coach program trains health coaches among other practitioners, and says each graduate must assess their own legal scope of practice (AIP Certified Coach, n.d.). That certificate does not change the scope described above: the coach supports the client’s own decisions and their clinician’s plan, and does not run the protocol.

Who does what

The physician

Usually a primary care physician first, then the specialist for the condition: a gastroenterologist for Crohn’s disease or ulcerative colitis, an endocrinologist for Hashimoto’s thyroiditis, a rheumatologist for rheumatoid arthritis or lupus, a dermatologist for psoriasis. Confirms the diagnosis and manages the treatment, which a diet does not replace; the rheumatology guideline frames its diet advice as used in conjunction with disease-modifying drugs (England et al., 2023). Tests for celiac disease before gluten is removed when that is a question. Monitors the labs that a large change in eating can affect: for thyroid conditions, thyroid hormone levels and any dose of thyroid hormone; for inflammatory bowel disease, markers of inflammation and nutrient levels such as vitamin D and iron, which the gastroenterology guidance says should be monitored in everyone with the condition (Hashash et al., 2024). Decides about steroids, mesalamine, biologics and anti-inflammatory painkillers.

The registered dietitian

Decides with the client and physician whether a restrictive trial makes sense at all, and if so designs it, ideally a dietitian experienced with the condition. Plans for the nutrients the removed foods supplied, above all calcium, vitamin D and iodine; adapts food texture for someone with a bowel stricture; and plans and paces reintroduction so the diet widens again. The gastroenterology guidance suggests that everyone newly diagnosed with inflammatory bowel disease have access to a registered dietitian and that people with complicated disease be co-managed with one (Hashash et al., 2024), and the rheumatology guideline recognizes the dietitian’s expert role on the team (England et al., 2023).

Other professionals

A psychologist or eating disorder specialist when food has become a source of fear or distress, or when restriction is growing. The kidney care team for anyone with kidney disease. An allergist for anyone with a food allergy.

The health and wellness coach

Helps the client get clear on what they hope the diet will do, what their clinicians know about it, and how they will judge whether it is helping. Helps with the practical habits a planned trial depends on: meal planning and batch cooking, shopping within a budget, packing food for work, handling restaurants, travel and family meals, and keeping the appointments that carry the client through reintroduction. Explores how the plan fits the client’s values, culture and household, and supports the sleep, stress and activity habits that clients often pursue alongside it. Notices whether eating is widening or narrowing over time, and holds the referral line when a question belongs to a clinician.

What a client bringing this diet needs

Clients usually arrive living with a diagnosis that affects their energy, pain, digestion or skin, often after years of symptoms, and many have found the diet online or through a community of people with the same condition. Some want relief that their treatment has not fully given them. Some want a sense of control. Some are already deep into elimination and are tired, anxious about reintroducing foods, or unsure whether it is working. Some are considering cutting back a medicine because they feel better. Each needs something different: a steady place to plan, help using their clinicians and a dietitian for the parts that belong to them, or a conversation about involving their care team before going further.

What the coaching conversation adds is room to look at the person’s whole life around the diet and to keep its endpoint in view. The diet is designed to end with reintroduction, and the coach can help a client keep the plan time-limited and connected to their care team rather than drifting into a long, narrowing restriction that no one planned.

What to ask

• “What are you hoping this will change for you, and how will you know if it is helping?”
• “Who on your care team knows you are doing this, and what did they say about it?”
• “How is this way of eating fitting with your household, your budget and your work?”

Referral red flags

A client with Crohn’s disease who reports severe or worsening abdominal pain, vomiting, or a sudden change in bowel habits after changing what they eat needs prompt medical care, through their own care plan or emergency help if the symptoms are severe; in the inflammatory bowel disease study, a participant with a known narrowing of the bowel was hospitalized with a partial blockage after greatly increasing raw vegetables, salad and meat (Konijeti et al., 2017). Worsening bowel symptoms, blood in the stool, or a flare during the diet go to the gastroenterologist. A client who has an allergic-type reaction after eating a food, especially one just reintroduced, needs emergency help if it is severe, using their own emergency plan if they have one; the Elimination Diets page describes the signs, and any food that has caused an allergic reaction comes back only through the allergist.

A client who says they have reduced or stopped a medicine because they feel better, or who wants to, is a reason to bring it to the prescriber; in an online survey of people with inflammatory bowel disease using AIP, 32 percent reported discontinuing steroids (Lee et al., 2019), and in the thyroid study several women’s thyroid hormone doses were lowered (Abbott et al., 2019). A client losing weight without meaning to, a child who is not growing as expected, or a client whose symptoms have not changed after the planned weeks goes to their clinician. So does a client taking thyroid hormone whose symptoms change during the diet.

A client taking insulin or a sulfonylurea who is about to make a substantial change in eating keeps the prescriber informed before making it. A client who reports shakiness, sweating or confusion may be having a low blood sugar episode right now; the first step is the one in their own diabetes plan for treating it, with emergency help if symptoms are severe or the person cannot manage the episode under their plan, and telling the prescriber is the separate step that follows. A client who has stayed in elimination well beyond the plan, or whose list of avoided foods keeps growing, is worth asking about it, as described under Signs it is going wrong in section 6.

Special populations

Pregnancy and breastfeeding

The searches for this page found no study of the diet in pregnancy or breastfeeding, and the published studies excluded pregnant and breastfeeding participants (Abbott et al., 2019; Ihnatowicz et al., 2023; Konijeti et al., 2017; Pardali et al., 2025). Iodine needs rise in pregnancy, to 220 micrograms a day, and the federal fact sheet names people who eat few or no dairy products, seafood and eggs among those who might not get enough (National Institutes of Health Office of Dietary Supplements, 2024); the elimination phase removes dairy and eggs but keeps seafood. In a qualitative study of women using fertility treatment, some had adopted AIP, and one described losing so much weight that her diet had to be changed (Claydon et al., 2026). Any restrictive diet before or during pregnancy, or while breastfeeding, belongs with the obstetric clinician and a registered dietitian.

Children and adolescents

The searches for this page found no study of the diet in children or adolescents. A 2024 report of children with iodine deficiency and an underactive thyroid included a 12-year-old girl with thyroid antibodies whose diet history included AIP and who had started salt loading on a naturopathic doctor’s advice; her iodine and thyroid levels returned to normal after kelp supplements and more fish were added (Patel et al., 2024). A single case cannot show how often this happens, but it shows why a child’s restricted diet belongs with the family, the pediatric clinician and a dietitian.

Older adults

The searches for this page found no study designed for older adults, and the studies reviewed did not report results for older adults separately. Whether a restricted diet meets an older adult’s needs for protein, calcium and vitamin D is a question for a dietitian, and new symptoms later in life are a reason for a clinical evaluation first.

Athletes and people with high activity

The searches for this page found no study of the diet in athletes. Removing grains, legumes and most starchy staples other than roots while training hard raises questions of energy and carbohydrate that belong to a sports dietitian.

People taking medication for diabetes, blood pressure, or blood thinning

The searches for this page found no study of the diet in people taking these medicines, and some studies excluded them (Abbott et al., 2019). Removing grains and legumes can substantially change carbohydrate intake, and a large rise in leafy green vegetables can change vitamin K intake; in the rheumatoid arthritis study, median vegetable intake rose from 4.5 to 11.5 servings a day (McNeill et al., 2026a). A client on insulin, a sulfonylurea, blood pressure medication or warfarin who plans a substantial change in eating keeps the prescriber informed before making it, rather than asking permission for every food choice.

People with a history of disordered eating

The diet’s rules and long list of removed foods have features that can feed restrictive eating. A 2025 review states that people with eating disorders or who are prone to orthorexia, an unhealthy fixation on eating only foods seen as pure, “may find the nature of the AIP restrictive and potentially triggering” (Pardali et al., 2025), and the main promoter says a person in recovery from an eating disorder may not be ready for it (Trescott, 2026). The searches for this page found no study that measured disordered eating in people following the diet. For a client with a current or past eating disorder, whether the diet is appropriate is a decision for the clinical team.

People with kidney disease

A university trial of the diet in IgA nephropathy, a kidney disease, was registered in 2025 and withdrawn in 2026, with “unable to recruit” as the reason (University of California, Los Angeles, 2025); the main promoter’s site still describes it as enrolling (Trescott, n.d.-b). The searches for this page found no published study of the diet in kidney disease. Needs in kidney disease depend on stage, lab results and dialysis, so any change in diet is planned with the kidney care team.

Vegetarians and vegans

Core AIP removes many foods commonly used as vegan protein sources, including legumes, soy, nuts and seeds, and it also removes the eggs and dairy many vegetarians rely on (Trescott, n.d.-a). A client combining those restrictions needs assessment of adequacy by a registered dietitian.

Client misconceptions

Three come up most. The first is that research has shown AIP works for autoimmune disease. The studies are small, short, and without comparison groups, so they cannot separate the diet from the support, the passage of time and the other changes that came with it; no randomized trial was found. The second is that feeling better on the diet means a food was the cause. The diet changes many things at once, including more vegetables, less added sugar, weight change, more support and attention to sleep and stress, and in the thyroid studies the main thyroid antibody did not fall (Abbott et al., 2019; Ihnatowicz et al., 2023).

The third is that feeling better is a reason to cut back medicine. Medicine decisions belong to the prescriber, and the main promoter itself says the diet is not a replacement for medication (Trescott, 2026). Each is taken up in section 6. The separate belief that nightshade vegetables cause inflammation is taken up on the Anti-Inflammatory Diet page.

🤝 COACHING CONNECTION

Rachel has Hashimoto’s thyroiditis and tells her coach she has been on the AIP elimination phase for 4 months. She feels less tired, but she is afraid to bring foods back and has also started taking a smaller dose of her thyroid pill on the days she feels good. The coach reflects how much the improvement means to her and asks what her doctor knows about the diet and the pill. Rachel says she has not mentioned either. The coach asks what she would want her doctor to know. Rachel decides to call the clinic about her thyroid dose and to ask for a referral to a dietitian about reintroduction. The coach did not comment on the dose, suggest a food to reintroduce, or say whether the diet was working.

4. The evidence

(select the heading to open or close this section)

The research on this diet is small and early. The searches for this page found 7 published reports from 4 groups of patients, plus an online survey of users: one group of 15 adults with inflammatory bowel disease, reported in 3 papers; 2 groups of adults with Hashimoto’s thyroiditis, of 16 and 28, each reported once; and one group of 9 adults with rheumatoid arthritis, reported in 2 papers. None had a concurrent comparison group, and none lasted longer than 12 weeks on the diet. They reported improvements in symptoms and quality of life, but they cannot show that the diet caused them. Each condition is reported separately below, by population. The ratings, all very low or not rated, are collected in the review record at the end of the page.

Evidence from randomized controlled trials

A trial that assigns people to the diet by chance and compares them with people assigned to something else is the strongest way to test whether the diet itself causes a result. The searches for this page, run in Europe PMC and the ClinicalTrials.gov registry on October 21, 2026, and run again on November 8, 2026, found no randomized trial of the autoimmune protocol for any condition. The registry lists 2 trials of the diet: the completed inflammatory bowel disease study described below, which had a single group, and a kidney disease trial that was withdrawn before enrolling anyone (University of California, Los Angeles, 2025). Reviews of diets for inflammatory bowel disease and of the diet itself reach the same point: the evidence is limited and controlled trials are needed (Gleave et al., 2025; Pardali et al., 2025).

Evidence from single-group studies

Every study of this diet followed one group of people before and after they changed what they ate. That design can show what happened to the people in the study, but not what would have happened without the diet. People often join such a study when their symptoms are bad, and symptoms that come and go tend to ease on their own over the following weeks, so improvement is expected even without a real effect. Participants also knew what they were eating, reported most outcomes themselves, and received intensive coaching, dietitian support and an online group alongside the diet. The studies therefore test a supported program, not the foods alone.

Inflammatory bowel disease

The first study enrolled adults with active Crohn’s disease or ulcerative colitis at a gastroenterology clinic in California, all with objective signs of inflammation on endoscopy or a raised fecal calprotectin, a stool marker of gut inflammation. Of 18 enrolled, 3 withdrew before starting, leaving 15: 9 with Crohn’s disease and 6 with ulcerative colitis, with an average of 19 years since diagnosis, and 7 taking a biologic medicine. They followed a 6-week elimination phase and then 5 weeks of holding it, with a health coach, a registered dietitian and a private online group. Clinical remission, judged by standard symptom-based scores, was reached by 11 of the 15 by 6 weeks, and all 11 stayed in remission to 11 weeks (Konijeti et al., 2017).

The objective measures were less clear. C-reactive protein, a blood marker of inflammation, did not change significantly. In the 6 people in remission who gave stool samples at both times, mean fecal calprotectin fell from 471 to 111 micrograms per gram, a change that was not statistically clear. Only 7 of the 15 had a follow-up endoscopy, and 6 of them showed some improvement. The study also started vitamin D and iron for people found to be low in them, and 2 participants had begun a biologic medicine within the 3 months before the study, although results excluding them were similar. The authors list the small size, the lack of a control group or blinding, and possible selection of motivated participants as limitations (Konijeti et al., 2017).

Two harms were reported, both in people with Crohn’s disease and a narrowed section of bowel. One was hospitalized with a partial bowel blockage about 3 weeks in, which the authors attributed to a large increase in raw vegetables, salad and meat without consulting the coach or dietitian; another withdrew because symptoms worsened (Konijeti et al., 2017). The gastroenterology guidance makes the same point for everyone with a stricture: such patients “may not tolerate fibrous, plant-based foods (ie, raw fruits and vegetables)” because of their texture (Hashash et al., 2024).

The same group reported quality of life in a second paper. Scores on a 10 to 70 inflammatory bowel disease questionnaire rose from an average of 46.5 at the start to 54.0 at 3 weeks and 60.5 at 11 weeks, but the number answering fell from 13 at the start to 4 by the last 2 surveys. The paper reports the change among those 4 both as P = 0.03 and as P = 0.07 in different places, depending on the test (Chandrasekaran, Groven, et al., 2019). With so few people answering at the end, this page does not rate the result. A third paper looked at gene activity in gut biopsies from 4 participants with ulcerative colitis before and after the diet (Chandrasekaran, Molparia, et al., 2019); section 5 describes it.

A separate online survey reached 78 people with inflammatory bowel disease who used the diet, recruited through AIP newsletters and support groups. Of them, 73 percent said they believed they had reached remission because of the diet, and 32 percent said they had stopped steroids after starting it (Lee et al., 2019). That is a self-selected group reporting its own experience, published as a conference abstract, so it shows how users describe the diet rather than what the diet does. Only the abstract was read. The published correction changes the author list, not the survey results (“Corrigendum,” 2019).

Reviews place this evidence in context. A 2025 systematic review of diets for active inflammatory bowel disease in adults, which included this diet among 10 studied diets, concluded that there is limited evidence to support any specific diet for mild to moderate disease (Gleave et al., 2025). It discusses the reports from the first study of this diet as if they corroborated each other, but they describe the same group of 15 people, which this page counts as one study.

A 2026 review notes that elimination patterns such as autoimmune protocol diets lack robust clinical trial data in inflammatory bowel disease, and that sustained elimination diets carry risks including malnutrition, micronutrient deficiency, food anxiety and avoidant/restrictive food intake disorder (Cunha et al., 2026). A 2026 scoping review, with searches updated to May 2026, found only the reports from the first study for this diet; it concluded that restrictive diets such as this one may help some patients but carry a risk of nutritional deficiencies and are not appropriate for widespread recommendation without professional supervision (Ingridsdotter et al., 2026).

The 2024 gastroenterology guidance, which states that no diet has consistently been found to decrease the rate of flares in adults, advises a Mediterranean diet for all patients unless there is a contraindication (Hashash et al., 2024). The Mediterranean Diet and Low-FODMAP Diet pages carry the evidence for those diets.

Hashimoto’s thyroiditis

Hashimoto’s thyroiditis is an autoimmune condition of the thyroid gland and a common cause of an underactive thyroid. A 2019 study enrolled 17 women aged 20 to 45 with the condition, who were not obese and had no other major conditions, recruited through social media and local practitioners, and 16 completed a 10-week online coaching program in the diet: 6 weeks of staged elimination and 4 weeks of holding it, led by health coaches and nutritional therapy practitioners with a physician (Abbott et al., 2019).

All 8 subscales of a standard quality of life questionnaire improved; for example, the median general health score rose from 40 to 70 on a 0 to 100 scale. A symptom questionnaire score fell from an average of 92 to 29. The thyroid measures did not change: thyroid-stimulating hormone, thyroid hormone levels and the 2 thyroid antibodies, thyroid peroxidase antibodies (TPO) and thyroglobulin antibodies, were similar before and after. High-sensitivity C-reactive protein fell from 1.63 to 1.15 milligrams per liter in 14 women. Six of the 13 women taking thyroid hormone had their doses lowered during or after the program, and 2 whose doses changed were left out of the thyroid hormone analysis. No moderate or severe adverse effects were reported (Abbott et al., 2019).

The study’s design limits what it can show. The program combined the diet with coaching, a support group, sleep, stress and activity guidance, and individual advice drawn from stool and organic acid tests; weight also fell, from an average of 149.5 to 143.4 pounds. One author co-founded the company whose program was the intervention, and another was paid by that company as a medical advisor (Abbott et al., 2019). Those ties are a reason to look closely at choices such as who was recruited and how outcomes were reported, not proof that the results are wrong.

A 2023 study in Poland enrolled 28 adults with Hashimoto’s thyroiditis and normal thyroid function, 27 women and 1 man, and 20 completed 12 weeks on the diet. The researchers planned an individual menu for each person, held monthly online meetings, and let participants continue their usual supplements and medicines. Fewer people reported symptoms such as tiredness, from 82 to 29 percent, and impaired concentration, from 71 to 18 percent. Free T3 fell from an average of 3.31 to 2.88 picomoles per liter and free T4 from 1.36 to 1.20 nanograms per deciliter, both staying within the reference range; thyroid-stimulating hormone also fell, but not by a statistically clear amount. The thyroid gland became about 5 to 6 percent smaller on ultrasound (Ihnatowicz et al., 2023).

TPO antibodies rose on average from 210 to 294 IU/mL, a 40 percent rise that the paper’s own table shows was not statistically clear, although its abstract calls it significant; 2 later reviews also report it as not significant (Pardali et al., 2025; Ruggeri et al., 2026). Thyroglobulin antibodies changed little. Body weight fell from an average of 69.0 to 65.5 kilograms, which the authors read as an energy deficit even though the food records showed no clear fall in energy intake. The paper reports 20 completers but does not state the number in each analysis, and the authors list participant selection and self-reported answers among its limitations (Ihnatowicz et al., 2023).

Across the 2 studies, the main thyroid antibody did not fall, and the only changes in thyroid hormone levels came in the 2023 study, whose authors interpret its weight loss as a sign of a calorie deficit. A 2026 endocrinology review reads the hormone changes as “an adaptive response to the energy deficit rather than a direct dietary effect on thyroid function” (Ruggeri et al., 2026). A 2025 review of the diet also points out that the earlier study’s lifestyle components could have affected its results (Pardali et al., 2025). Removing gluten alone in Hashimoto’s thyroiditis without celiac disease has its own small trials, reported on the Gluten-Free Diet page.

Rheumatoid arthritis

A 2026 study in New Zealand enrolled 11 adults with rheumatoid arthritis on stable medication, and 9 completed it: 4 weeks on their usual diet, then 8 weeks on the diet, with a 1-hour instruction session from a registered nutritionist, a booklet and an online group. Participants rated their disease activity each week on 2 questionnaires scored from 0 to 10. Compared with their own 4 usual-diet weeks, the average disease activity score at the end of the diet was 1.52 points lower, with an interval from 0.14 to 2.90 points lower; 4 people had a change the authors rate as clinically meaningful, and 1 person got worse. Discretionary anti-inflammatory painkiller use fell (McNeill et al., 2026a).

The authors call these findings hypothesis-generating. About half of the participants started with low disease activity; the outcomes were self-reported; the diet always came after the usual-diet weeks, so changes over time cannot be separated from the diet; and a pandemic lockdown limited social eating. In the first weeks, 6 people had headaches and 7 had digestive symptoms such as bloating, which passed; 2 had persistent problems, one with diarrhea and one with loss of appetite and unintended weight loss; and 8 of the 9 lost weight, a mean of 5 kilograms (McNeill et al., 2026a). A 2025 scoping review by the same group, covering 48 records published from 1949 to 2024, including 20 intervention studies, found that research on elimination and reintroduction diets in rheumatoid arthritis lacks standardized protocols, uses dated methods and has little contemporary research; it includes no study of the autoimmune protocol (McNeill et al., 2025).

The American College of Rheumatology’s 2022 guideline, published in 2023, conditionally recommends a Mediterranean-style diet and conditionally recommends against other formally defined diets for managing rheumatoid arthritis, on very low to moderate certainty evidence, citing the lack of consistent, clinically meaningful benefit and the burden and costs of following such a diet. The diets it evaluated include paleo and elimination diets; AIP is not named (England et al., 2023). The guideline was read as the authors’ accepted manuscript, and its recommendations and evidence labels match the published version.

Other autoimmune conditions

The diet is promoted for many other conditions. A Cleveland Clinic article lists psoriatic arthritis, celiac disease, type 1 diabetes, psoriasis and multiple sclerosis among the conditions for which it is “perhaps most helpful” (Cleveland Clinic, 2023), and an analysis of online discussions about lupus found the diet occasionally framed as a curative alternative to treatment (Tang et al., 2026). The searches for this page found no published study of the diet in lupus or in any of those conditions. The main promoter describes a study in eczema and psoriasis completed in 2020 that has not been published (Trescott, n.d.-b), so it cannot be assessed. Celiac disease is treated with a lifelong gluten-free diet, described on the Gluten-Free Diet page; the multiple sclerosis trials of the Wahls diet, a different modified paleo diet, are on the Paleo Diet page.

Cardiometabolic outcomes

The searches for this page did not identify an AIP study measuring cardiovascular events. In the inflammatory bowel disease study, blood lipids did not change significantly as a group, but some participants had small rises in triglycerides or LDL cholesterol that led the dietitian and coach to modify their diets (Konijeti et al., 2017). The searches for this page found no other study that reported blood pressure, lipids or blood sugar as outcomes of the diet.

Cancer

The searches for this page found no study of the diet that measured cancer incidence, progression or survival. The studies reviewed here do not establish any effect on cancer in either direction.

Body weight, as measured

Weight was not the aim of any of these studies, and this page reports it only as something they measured. It did not change significantly in the inflammatory bowel disease study (Konijeti et al., 2017). It fell from an average of 149.5 to 143.4 pounds over 10 weeks in the 2019 thyroid study (Abbott et al., 2019), fell from an average of 69.0 to 65.5 kilograms over 12 weeks in the 2023 thyroid study (Ihnatowicz et al., 2023), and fell in 8 of the 9 people in the rheumatoid arthritis study, by a mean of 5 kilograms over 8 weeks (McNeill et al., 2026a).

In the rheumatoid arthritis study, one person’s appetite fell and their weight dropped without their meaning it to, and a year later that person had returned to unrestricted eating to regain weight (McNeill et al., 2026a, 2026b). Weight a person loses without meaning to is a reason to involve a clinician, and a child who is not growing as expected needs the pediatrician. Neither is a sign that the diet is working.

Mortality

The searches for this page found no study of the diet that measured death from any cause. Nothing in the studies reviewed here establishes an effect on survival in either direction.

Eating behavior and wellbeing

Quality of life rose in the 2019 thyroid study and in the inflammatory bowel disease study, among the few who answered at the end (Abbott et al., 2019; Chandrasekaran, Groven, et al., 2019), and fatigue and sleep scores improved in most of the rheumatoid arthritis participants (McNeill et al., 2026a). These are self-reported measures in people who knew their diet, collected without a comparison group. The interviews with rheumatoid arthritis participants describe the effort the diet took, the “diet fatigue” near the end, and fear of symptoms returning as one thing that kept people adherent (McNeill et al., 2026b). The searches for this page did not identify a study measuring disordered eating in people following the diet.

Evidence from long-term prospective cohort studies

A cohort study follows people forward over years and records what happens to them. The searches for this page found no long-term comparative cohort study of people following the autoimmune protocol. What exists instead is the single-group studies above and one online survey of users (Lee et al., 2019), which describe what happened to particular people but cannot show what the diet caused.

Highlighted studies

These 4 studies carry the most weight for this diet, one for each group of patients studied. Konijeti 2017, Abbott 2019 and McNeill 2026 were read in full in PubMed Central, and Ihnatowicz 2023 in full in the journal’s open-access copy.

On a narrow screen, scroll the table sideways to see every column.

Highlighted studies for the Autoimmune Protocol Diet

Study	Design	Sample size	Duration	Finding	The limitation that matters
Konijeti et al., 2017	Single-group study, open label, at 1 gastroenterology clinic	18 adults with active Crohn’s disease or ulcerative colitis enrolled; 15 began	6 weeks of elimination, then 5 weeks of holding it	11 of 15 in clinical remission by 6 weeks, all still in remission at 11 weeks; no clear change in C-reactive protein; 1 hospitalization for partial bowel blockage	No comparison group, so the change cannot be credited to the diet; symptom scores partly self-reported; vitamin D and iron replacement and coaching given alongside
Abbott et al., 2019	Single-group study of an online coaching program	17 women aged 20 to 45 with Hashimoto’s thyroiditis; 16 completed	10 weeks	Quality of life and symptom scores improved; thyroid hormones and antibodies did not change; 6 of 13 on thyroid hormone had doses lowered	No comparison group; the program’s company co-founder was an author and another author was paid by the company
Ihnatowicz et al., 2023	Single-group study	28 adults with Hashimoto’s thyroiditis and normal thyroid function enrolled; 20 completed	12 weeks	Fewer reported symptoms; free T3 and free T4 fell within the reference range; TPO antibodies rose 40 percent, not statistically clear; weight fell	No comparison group; 8 of 28 did not complete and the number in each analysis is not stated; menus individually planned by the researchers; the abstract calls the antibody rise significant, which the paper’s table does not support
McNeill et al., 2026a	Single-group study with a usual-diet run-in, open label	11 adults with rheumatoid arthritis enrolled; 9 completed	4 weeks usual diet, then 8 weeks on the diet	Self-rated disease activity 1.52 points lower on a 0 to 10 scale than during the usual-diet weeks, from 0.14 to 2.90 lower	Fixed order and self-reported outcomes, so time trends and expectation cannot be separated from the diet; about half had low disease activity at the start

Head to head

The searches for this page found no trial that compared the autoimmune protocol directly with another diet, with usual eating, or with medication in any condition. The rheumatoid arthritis study compared each person with their own earlier weeks on their usual diet, which is not a randomized comparison (McNeill et al., 2026a). Comparisons of the parent pattern with other diets are on the Paleo Diet page, and the multiple sclerosis trial comparing the Wahls diet with a low-saturated-fat diet is described there.

In inflammatory bowel disease, the Mediterranean diet is the pattern the gastroenterology guidance advises for most patients (Hashash et al., 2024), and in rheumatoid arthritis it is the only formally defined diet the rheumatology guideline recommends (England et al., 2023). The searches for this page did not identify a trial comparing either with this diet.

Where the evidence is absent

The searches for this page found no randomized trial of the diet, no study with a concurrent comparison group, no study longer than 12 weeks on the diet, and no long-term comparative cohort study. They found no published study in lupus, psoriasis, multiple sclerosis, celiac disease, type 1 diabetes or kidney disease; no study designed for children, pregnancy or breastfeeding, older adults or athletes; and no study of people taking diabetes, blood pressure or blood-thinning medication. The searches for this page did not identify an AIP study measuring cardiovascular events, cancer, death or disordered eating.

The searches found no study of Modified AIP, the 2024 version, and no study of the diet as people follow it on their own without coaching, a dietitian and a study team. They found one study that recorded nutrient intake before and during the diet, on menus its researchers planned (Ihnatowicz et al., 2023), and none that measured nutrient intake or status as people follow the diet on their own; the rheumatoid arthritis team says its nutrient analysis is reported in a separate paper, which the searches did not find (McNeill et al., 2026a). They found no study that tested whether foods identified during reintroduction cause symptoms when tested blind. For each condition, the evidence is a single small study, or 2 in Hashimoto’s thyroiditis, so the results cannot be checked against each other.

5. Mechanisms

(optional reading; select the heading to open or close this section)

This section explains how the diet is thought to work in the body. You can skip it. Nothing in the coaching sections depends on it.

Established mechanisms

Few mechanisms specific to this diet have been shown in people. What has been shown is that following it changes what people eat in measurable ways. In the rheumatoid arthritis study, median vegetable intake rose from 4.5 to 11.5 servings a day, fruit from 1 to 2.9, fiber from 25.5 to 35.6 grams a day, and added sugar fell from 31 to 17 grams a day, while refined grains fell to zero (McNeill et al., 2026a). Body weight fell in most of the studies (Abbott et al., 2019; McNeill et al., 2026a). Because so much about eating changes at once, including diet quality and, for many people, energy intake, the studies cannot attribute their results to removing particular foods.

Two other effects are well described. For people with celiac disease, gluten drives the intestinal damage, and removing it is the treatment; the Gluten-Free Diet page explains the mechanism, and the autoimmune protocol removes gluten along with much else but is not a substitute for the celiac care plan. And for people with a narrowed section of bowel, fibrous raw vegetables and fruit can be hard to tolerate because of their texture, and the gastroenterology guidance says that careful chewing, and cooking them to a softer consistency, may help such patients eat a wider variety of plant foods (Hashash et al., 2024).

Proposed mechanisms

The diet’s central rationale is proposed rather than established. Researchers describe it as starting from Loren Cordain’s hypothesis that components of certain foods, including lectins, glycoalkaloids in nightshades, casein, gluten, wheat germ agglutinin, egg white lysozyme and food additives, may make the gut lining more permeable or act as immune stimulants, so that food and bacterial fragments reach the circulation and contribute to autoimmune activity; Ballantyne expanded the rationale for each exclusion (McNeill et al., 2026a). A 2025 review describes increased gut permeability and an imbalance of gut bacteria as possible environmental triggers of autoimmunity in genetically susceptible people, while cautioning that classifying gut bacteria simply as good or bad is misleading (Pardali et al., 2025). The searches for this page found no study of the diet that measured gut permeability.

The one mechanistic study of the diet looked at gene activity in colon biopsies from 4 people with ulcerative colitis before and after it. It found 324 genes whose activity changed, with groups of genes linked to immune and inflammatory processes changing in both directions (Chandrasekaran, Molparia, et al., 2019). With 4 people and no comparison group, and with most of them improving clinically at the same time, the changes cannot be separated from the remission itself. The thyroid hormone changes in the 2023 study have been read as a response to lower energy intake rather than a direct effect of the foods removed (Ruggeri et al., 2026).

One more mechanism applies to every open diet: expectation and attention. When a person knows what they have removed, is supported closely by coaches and peers, and rates their own symptoms, what they notice can be shaped by what they expect. A proposed mechanism never supports a claim in section 4.

6. Risks, contraindications and myths

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Warnings from professional or regulatory bodies

The searches for this page found no regulatory warning about the autoimmune protocol itself. Two professional bodies make statements that apply to it. The American College of Rheumatology states that “adherence to a formally defined diet, other than a Mediterranean-style diet, is conditionally recommended against” for managing rheumatoid arthritis, based on very low to moderate certainty evidence of no consistent, clinically meaningful benefit and on the burden and costs of such diets; its list of evaluated diets names paleo and elimination diets but not this one (England et al., 2023). The American Gastroenterological Association advises that people with inflammatory bowel disease and symptomatic strictures may not tolerate fibrous, raw plant foods, and that careful chewing and cooking them to a softer consistency may help (Hashash et al., 2024).

The federal fact sheet on iodine adds a caution relevant to people with Hashimoto’s thyroiditis who change their iodine intake: “Some people, such as those with autoimmune thyroid disease and iodine deficiency, may experience adverse effects with iodine intakes considered safe for the general population” (National Institutes of Health Office of Dietary Supplements, 2024). How much iodine a person with a thyroid condition needs, from food or supplements such as kelp, is a question for the physician and a dietitian.

Nutrient gaps

The gaps depend on how many foods are removed and for how long. Calcium is the clearest. Milk, yogurt and cheese contain high amounts of calcium, and the federal fact sheet lists, as other sources, certain vegetables such as kale, broccoli and Chinese cabbage, canned sardines and salmon with bones, and fortified foods such as many fruit juices, milk substitutes, tofu and cereals (National Institutes of Health Office of Dietary Supplements, 2026). The elimination phase removes dairy, tofu, cereals and most fortified milk substitutes, leaving vegetables, canned fish with bones and any fortified juice. In the 2023 thyroid study, whose menus were planned by the researchers, recorded calcium intake fell from an average of 654 to 477 milligrams a day (Ihnatowicz et al., 2023), against a recommended intake of 1,000 milligrams a day for adults aged 19 to 50 (National Institutes of Health Office of Dietary Supplements, 2026).

Iodine is the second. The federal fact sheet names seaweed as one of the best food sources, with fish, seafood, eggs and dairy, notes that specialty salts such as sea salt, kosher salt and Himalayan salt are not usually iodized, and names people who eat few or no dairy products, seafood and eggs among those at risk of inadequate intake (National Institutes of Health Office of Dietary Supplements, 2024). The elimination phase removes dairy and eggs but keeps seafood and sea vegetables, so a person’s iodine intake depends on how much of those they eat and what salt they use. In the 2023 thyroid study, recorded iodine intake rose from 118 to 188 micrograms a day, and the authors suggest the higher intake may have played a part in the thyroid changes they saw, a possibility the study did not test (Ihnatowicz et al., 2023).

A 2025 review adds that removing grains might lower intakes of thiamin, riboflavin, niacin, fiber and iron, and removing dairy may lower vitamin D and calcium, while noting that the risk depends on how strictly the diet is followed and that adequacy has not been studied well (Pardali et al., 2025). In the inflammatory bowel disease study, vitamin D and iron were started for people found low in them at the start (Konijeti et al., 2017). Fiber, by contrast, rose in the rheumatoid arthritis study (McNeill et al., 2026a). The searches for this page found no current authority that sets nutrient numbers for this diet; what replaces each removed food is a question for a registered dietitian.

Who should not follow it without medical supervision

Anyone using the diet for a diagnosed condition should do so with the clinician who treats that condition, because any change to the condition’s treatment is that clinician’s decision. Supervision matters most for people with Crohn’s disease and a known stricture, who had the harms reported in the inflammatory bowel disease study (Konijeti et al., 2017; Hashash et al., 2024); for people taking thyroid hormone, whose doses were changed during a study (Abbott et al., 2019); and for people taking steroids, mesalamine or other medicines for their condition, which some users report stopping (Lee et al., 2019).

It also matters for children, as the single case of iodine deficiency shows (Patel et al., 2024); for people who are pregnant, breastfeeding or trying to conceive, whose iodine needs are higher (National Institutes of Health Office of Dietary Supplements, 2024); for people with kidney disease, whose needs depend on stage, lab results and dialysis; for people with a current or past eating disorder (Pardali et al., 2025); for vegetarians and vegans (Trescott, n.d.-a); and for anyone taking insulin, a sulfonylurea, blood pressure medication or warfarin, who keeps the prescriber informed before a substantial change in eating. The special populations list in section 3 is built from these cautions.

Medication interactions

The searches for this page found no medicine whose dose is known to change because of this diet itself; the practical issues are indirect. Thyroid hormone doses were lowered for 6 of 13 women in the 2019 thyroid study, some because of laboratory results before the program started (Abbott et al., 2019), and thyroid hormone levels fell in the 2023 study (Ihnatowicz et al., 2023). A client taking levothyroxine or another thyroid hormone medicine contacts the prescriber before a substantial change in eating. The prescriber decides what monitoring is needed and reviews changes in supplements, including calcium, and their timing. The coach does not order or interpret thyroid tests or change medication.

In the inflammatory bowel disease study, 2 participants stopped oral mesalamine on their own despite advice to keep medicines stable (Konijeti et al., 2017). The federal calcium fact sheet notes that calcium carbonate supplements can interfere with the absorption of levothyroxine, a thyroid hormone, so a calcium supplement added to replace dairy is something the prescriber should know about (National Institutes of Health Office of Dietary Supplements, 2026).

The diet asks people to avoid nonsteroidal anti-inflammatory painkillers; whether a person takes them, and what replaces them for pain, is the prescriber’s question, particularly for someone with rheumatoid arthritis. Removing grains and legumes can change carbohydrate intake, which matters for insulin and sulfonylureas, and a large rise in leafy vegetables can change vitamin K intake, which matters for warfarin. A coach never adjusts medication; the point of knowing these is to know when to send the client back to the prescriber.

Signs it is going wrong

Physical signs that need the client’s care plan, a medical assessment or emergency help include severe or worsening abdominal pain, vomiting, or a sudden change in bowel habits, above all in someone with Crohn’s disease; blood in the stool or a flare of the condition; an allergic-type reaction to a reintroduced food, which calls for the client’s emergency plan and emergency help if severe; persistent diarrhea, loss of appetite or tiredness; weight lost without meaning to; a child who is not growing as expected; and new symptoms in someone taking thyroid hormone. A client on diabetes medication who reports shakiness, sweating or confusion treats a possible low blood sugar episode first under their own plan, with emergency help if symptoms are severe or the episode cannot be managed, and then tells the prescriber. Each of these is a reason to involve a clinician, not a diagnosis.

Eating behavior needs separate care, because removing foods is the point of the diet. What carries meaning is restriction that outlasts its plan: staying in elimination for months beyond the 30 to 90 days its own promoter describes (Trescott, n.d.-a), fearing or skipping reintroduction, a list of avoided foods that keeps growing, describing foods as safe and unsafe, or turning down meals with other people. Many have ordinary reasons, such as a clinician’s plan, a confirmed food allergy, a work schedule, food access, cultural practice or household preferences, so a behavior alone tells a coach little. The coach asks what the behavior is for, whether it causes distress, whether it is narrowing what the person eats, and whether it is getting in the way of daily life. A real concern goes through the coach’s own referral process, or to the client’s clinician under an existing care plan.

Myths and where they came from

Myth: research shows AIP puts autoimmune disease into remission

Where it came from: the promoters’ summaries of the first study, in which 73 percent of 15 people with inflammatory bowel disease reached clinical remission (Konijeti et al., 2017; Trescott, 2026). What is true: that study had no comparison group, gave vitamin D, iron and intensive support alongside the diet, and measured remission mainly by symptom scores; the authors called for randomized trials. No randomized trial was found for any condition, and in the thyroid studies the main thyroid antibody did not fall (Abbott et al., 2019; Ihnatowicz et al., 2023).

Myth: the diet heals a leaky gut, and that is what calms autoimmunity

Where it came from: the diet’s founding rationale, from Cordain’s hypothesis and Ballantyne’s books (McNeill et al., 2026a). What is true: increased gut permeability is a proposed contributor to autoimmunity, but the searches for this page found no study of the diet that measured gut permeability, and the only mechanistic study examined gene activity in 4 people (Chandrasekaran, Molparia, et al., 2019; Pardali et al., 2025).

Myth: if I feel better, I can cut back my medicine

Where it came from: reports of thyroid dose reductions and of users stopping steroids (Abbott et al., 2019; Lee et al., 2019). What is true: in the thyroid study, doses were lowered after laboratory testing within a program run with a physician, and the promoter itself says the diet is not a replacement for medication (Abbott et al., 2019; Trescott, 2026). Medicine decisions belong to the prescriber.

Myth: the foods that bring back symptoms in reintroduction are proven triggers

Where it came from: the protocol’s reintroduction phase, in which people test one food at a time and record symptoms (Trescott, n.d.-c). What is true: reintroduction in this diet is open, so the person knows what they are eating, and the searches for this page found no study that checked foods identified this way in blind tests. The Elimination Diets page explains why clinicians use blinded challenges when they need a firm answer.

7. Key terms

Autoimmune protocol (AIP)

A strict, phased version of the paleo diet that removes many food groups for a period and then reintroduces them one at a time, promoted for autoimmune conditions.

Autoimmune condition

A condition in which the immune system attacks the body’s own tissues, such as Hashimoto’s thyroiditis, rheumatoid arthritis or lupus.

Elimination phase

The period, usually described as 30 to 90 days, in which all the listed foods are removed.

Reintroduction phase

The period in which removed foods are brought back one at a time while symptoms are recorded.

Core AIP and Modified AIP

The original, fully restricted elimination list, which its main promoter says was used in all the published studies, and a less strict version introduced in 2024 that allows rice, pseudo-grains, most legumes, seeds and ghee.

Nightshades

A plant family that includes tomatoes, potatoes, peppers, eggplant and the spices made from them, such as paprika and cayenne.

Inflammatory bowel disease

Crohn’s disease and ulcerative colitis, chronic immune-driven inflammation of the digestive tract.

Stricture

A narrowed section of bowel, which can make fibrous foods hard to pass.

Clinical remission

In these studies, a symptom-based disease activity score below a set cutoff, not necessarily healing seen on endoscopy.

Fecal calprotectin

A protein measured in stool that rises with inflammation in the gut.

Hashimoto’s thyroiditis

An autoimmune condition of the thyroid gland that is a common cause of an underactive thyroid.

Thyroid antibodies

Antibodies against thyroid proteins, such as thyroid peroxidase (TPO) and thyroglobulin, that mark autoimmune thyroid disease.

Single-group study

A study that measures one group before and after a change, without a comparison group, so it cannot show what would have happened without the change.

Leaky gut

A popular term for increased permeability of the gut lining, proposed but not shown to be how this diet works.

Orthorexia

An unhealthy fixation on eating only foods a person considers pure or healthy.

8. Review questions

1. What does the elimination phase of the autoimmune protocol remove, and how does Modified AIP differ from Core AIP? Why does it matter which “maintenance” phase a client means?
2. For readers who open section 4: in the inflammatory bowel disease study, how many people were studied, for how long, and why can its 73 percent remission figure not show that the diet caused remission?
3. In the 2 Hashimoto’s thyroiditis studies, what happened to quality of life, to the main thyroid antibody and to thyroid medication? What other changes during the programs could explain the improvements?
4. A client with Crohn’s disease tells you she is starting AIP and plans to eat large raw salads every day. What do you ask, and where is the referral line?
5. Pick one myth from section 6. Explain where it came from and what the evidence shows instead.

9. References

Abbott, R. D., Sadowski, A., & Alt, A. G. (2019). Efficacy of the autoimmune protocol diet as part of a multi-disciplinary, supported lifestyle intervention for Hashimoto’s thyroiditis. Cureus, 11(4), Article e4556. https://doi.org/10.7759/cureus.4556

AIP Certified Coach. (n.d.). AIP Certified Coach practitioner training. Retrieved November 8, 2026, from aipcertified.com/training

Autoimmune Wellness. (n.d.). The history of the AIP movement (2011 to present). Retrieved November 8, 2026, from autoimmunewellness.com/history-aip-movement-2011-to-present

Ballantyne, S. (n.d.). From ThePaleoMom to Nutrivore. The Paleo Mom. Retrieved November 8, 2026, from thepaleomom.com/from-thepaleomom-to-nutrivore

Book Passage. (n.d.). The new autoimmune protocol: The complete guide to managing autoimmune disease, with 75 delicious recipes. Retrieved November 8, 2026, from bookpassage.com/book/9780593980835

Chandrasekaran, A., Groven, S., Lewis, J. D., Levy, S. S., Diamant, C., Singh, E., & Konijeti, G. G. (2019). An autoimmune protocol diet improves patient-reported quality of life in inflammatory bowel disease. Crohn’s & Colitis 360, 1(3), Article otz019. https://doi.org/10.1093/crocol/otz019

Chandrasekaran, A., Molparia, B., Akhtar, E., Wang, X., Lewis, J. D., Chang, J. T., Oliveira, G., Torkamani, A., & Konijeti, G. G. (2019). The autoimmune protocol diet modifies intestinal RNA expression in inflammatory bowel disease. Crohn’s & Colitis 360, 1(3), Article otz016. https://doi.org/10.1093/crocol/otz016

Claydon, E. A., Davidson, D., McCarty, K. M., & Wang, J. (2026). “There is something that I can control”: Food, fertility, and the journey to pregnancy. Journal of Health, Population and Nutrition, 45(1), Article 133. https://doi.org/10.1186/s41043-026-01317-7

Cleveland Clinic. (2023, June 28). A little of this and that: Your guide to the AIP diet. Health Essentials. health.clevelandclinic.org/aip-diet-autoimmune-protocol-diet

Corrigendum: Clinical course and dietary patterns among patients incorporating the autoimmune protocol for management of inflammatory bowel disease (P12-010-19). (2019). Current Developments in Nutrition, 3(10), Article nzz118. https://doi.org/10.1093/cdn/nzz118

Cunha, B., Alter, A., Berschback, M., Park, S., Gold, S., & Schneider, Y. (2026). Rethinking restrictive diets in IBD: Toward an inclusion-focused nutritional paradigm. Current Gastroenterology Reports, 28(1), Article 31. https://doi.org/10.1007/s11894-026-01047-0

England, B. R., Smith, B. J., Baker, N. A., Barton, J. L., Oatis, C. A., Guyatt, G., Anandarajah, A., Carandang, K., Chan, K. K., Constien, D., Davidson, E., Dodge, C. V., Bemis-Dougherty, A., Everett, S., Fisher, N., Fraenkel, L., Goodman, S. M., Lewis, J., Menzies, V., . . . Treadwell, J. R. (2023). 2022 American College of Rheumatology guideline for exercise, rehabilitation, diet, and additional integrative interventions for rheumatoid arthritis. Arthritis & Rheumatology, 75(8), 1299-1311. https://doi.org/10.1002/art.42507

Gleave, A., Shah, A., Tahir, U., Blom, J. J., Dong, E., Patel, A., Marshall, J. K., & Narula, N. (2025). Using diet to treat inflammatory bowel disease: A systematic review. American Journal of Gastroenterology, 120(1), 83-97. https://doi.org/10.14309/ajg.0000000000002973

Hashash, J. G., Elkins, J., Lewis, J. D., & Binion, D. G. (2024). AGA clinical practice update on diet and nutritional therapies in patients with inflammatory bowel disease: Expert review. Gastroenterology, 166(3), 521-532. https://doi.org/10.1053/j.gastro.2023.11.303

Ihnatowicz, P., Gębski, J., & Drywień, M. E. (2023). Effects of autoimmune protocol (AIP) diet on changes in thyroid parameters in Hashimoto’s disease. Annals of Agricultural and Environmental Medicine, 30(3), 513-521. https://doi.org/10.26444/aaem/166263

Ingridsdotter, J., Vejzovic, V., Elmerstig, E., & Sjöberg, K. (2026). Multiple paths to health: A scoping review of dietary interventions for adults with Crohn’s disease and ulcerative colitis. Therapeutic Advances in Gastroenterology, 19, Article 17562848261479366. https://doi.org/10.1177/17562848261479366

Jones, L. (2026, January 8). AIP diet 101: Advice, food lists and meal plans. U.S. News & World Report. health.usnews.com/best-diet/aip-diet

Konijeti, G. G., Kim, N., Lewis, J. D., Groven, S., Chandrasekaran, A., Grandhe, S., Diamant, C., Singh, E., Oliveira, G., Wang, X., Molparia, B., & Torkamani, A. (2017). Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflammatory Bowel Diseases, 23(11), 2054-2060. https://doi.org/10.1097/MIB.0000000000001221

Lee, J., Pedretti, C., & Konijeti, G. (2019). Clinical course and dietary patterns among patients incorporating the autoimmune protocol for management of inflammatory bowel disease (P12-010-19) [Abstract]. Current Developments in Nutrition, 3(Suppl. 1), Article nzz035.P12-010-19. https://doi.org/10.1093/cdn/nzz035.P12-010-19

Lichtenstein, A. H., Khera, A., Anderson, C. A. M., Appel, L. J., DeSilva, D. M., Gardner, C., Hu, F. B., Jones, D. W., Petersen, K. S., & American Heart Association. (2026). 2026 dietary guidance to improve cardiovascular health: A scientific statement from the American Heart Association. Circulation, 153(18), e1285-e1295. https://doi.org/10.1161/CIR.0000000000001435

McNeill, J., Zinn, C., Mearns, G., & Grainger, R. (2025). Elimination reintroduction diets and oral food challenge in adults with rheumatoid arthritis: A scoping review. Nutrition Research Reviews, 38(2), 699-716. https://doi.org/10.1017/s0954422425000083

McNeill, J. J., Mearns, G. J., Grainger, R., & Zinn, C. (2026a). The effect of an autoimmune protocol (AIP) diet in adults with rheumatoid arthritis: A single arm crossover pilot feasibility study. Musculoskeletal Care, 24(2), Article e70214. https://doi.org/10.1002/msc.70214

McNeill, J., Mearns, G. J., Grainger, R., & Zinn, C. (2026b). Exploring participant experiences with the autoimmune protocol (AIP) diet in rheumatoid arthritis: A longitudinal qualitative study. Journal of Nutritional Science, 15, Article e73. https://doi.org/10.1017/jns.2026.10135

National Institutes of Health Office of Dietary Supplements. (2024, November 5). Iodine: Fact sheet for health professionals. https://ods.od.nih.gov/factsheets/Iodine-HealthProfessional/

National Institutes of Health Office of Dietary Supplements. (2026). Calcium: Fact sheet for health professionals. ods.od.nih.gov/factsheets/Calcium-HealthProfessional

Pardali, E. C., Gkouvi, A., Gkouskou, K. K., Manolakis, A. C., Tsigalou, C., Goulis, D. G., Bogdanos, D. P., & Grammatikopoulou, M. G. (2025). Autoimmune protocol diet: A personalized elimination diet for patients with autoimmune diseases. Metabolism Open, 25, Article 100342. https://doi.org/10.1016/j.metop.2024.100342

Patel, T., Longendyke, R., Kanakatti Shankar, R., & Merchant, N. (2024). Iodine deficiency hypothyroidism in children in recent years: A re-emerging issue? Endocrinology, Diabetes & Metabolism Case Reports, 2024(2), Article 24-0038. https://doi.org/10.1530/EDM-24-0038

Ruggeri, R. M., Virili, C., Mocini, E., Campennì, A., Centanni, M., Rotondi, M., Cannavò, S., Croce, L., & Migliaccio, S. (2026). The role of nutrition on thyroid health and disease: Myths and facts. Journal of Endocrinological Investigation, 49(8), 1759-1779. https://doi.org/10.1007/s40618-026-02852-0

Tang, J., Jiang, H., Peng, J., Zhang, H., Qin, P., & Huang, Z. (2026). AI-driven topic modeling and sentiment analysis of systemic lupus erythematosus discussions on social media: Cross-platform study. Journal of Medical Internet Research, 28, Article e95175. https://doi.org/10.2196/95175

Trescott, M. (n.d.-a). The elimination phase of the Autoimmune Protocol (AIP). The Autoimmune Protocol. Retrieved November 8, 2026, from theautoimmuneprotocol.com/aip-elimination-phase-guide

Trescott, M. (n.d.-b). Ongoing and forthcoming research on the Autoimmune Protocol. The Autoimmune Protocol. Retrieved November 8, 2026, from theautoimmuneprotocol.com/aip-ongoing-research

Trescott, M. (n.d.-c). The reintroduction phase of the Autoimmune Protocol (AIP). The Autoimmune Protocol. Retrieved November 8, 2026, from theautoimmuneprotocol.com/aip-reintroduction-phase-guide

Trescott, M. (2026). What is the Autoimmune Protocol? The complete guide to AIP. The Autoimmune Protocol. theautoimmuneprotocol.com/what-is-aip-autoimmune-protocol-guide

University of California, Los Angeles. (2025, June 15). Autoimmune protocol diet intervention on proteinuria in IgA nephropathy patients (ClinicalTrials.gov Identifier NCT07022574). ClinicalTrials.gov. clinicaltrials.gov/study/NCT07022574

Evidence rating and review record

Each row identifies the method, source, outcome or recommendation, and comparison being rated. Ratings from different tools are not interchangeable. The source is either a named published review or this page’s own judgment. The rating in the banner is for this diet’s main claimed outcome or recommendation, and the banner names the tool that produced it. A high rating means the research is solid; it does not mean the diet is right for everyone, and it does not mean a coach should recommend it.

The rated outcomes on this page use GRADE, the same 4-level scale as the clinical guidelines you will meet in practice. High means further research is very unlikely to change the conclusion. Moderate means further research may change it. Low means further research is likely to change it. Very low means the conclusion is uncertain. GRADE rates each outcome separately, so a diet can be high for one outcome and very low for another. A row marked Not rated is an abstention, not a certainty level, and a row marked provisional awaits a check of a source named in the row. Recommendations from guideline panels are in a separate second table.

No published review has rated the autoimmune protocol itself, so every outcome row is this page’s own judgment, assigned from the evidence with every GRADE domain recorded in the reasons. Every row concerns one condition in one population; none is a rating of the diet in general, and none applies to people without the condition studied.

On a narrow screen, scroll the table sideways to see every column.

Evidence ratings, their sources and reasons

Outcome	Certainty	Who rated it, and for which comparison	Why it is rated this way
Inflammatory bowel disease: observed clinical remission by 11 weeks during an AIP program added to usual medical care, adults with active Crohn’s disease or ulcerative colitis; no concurrent comparison group (the banner rating)	Very low	GRADE, this page’s own judgment, from 1 single-group study read in full (Konijeti et al., 2017): 18 enrolled, 15 began, 11 weeks. No comparison group was studied.	A study with no concurrent comparison group is assessed as nonrandomized evidence, which starts low. The certainty rated here is how sure one can be that the remission is attributable to the program; the observed proportion is not a causal estimate. Eleven of 15 participants were in remission, 73 percent, with an exact 95 percent interval of about 45 to 92 percent for that observed proportion, calculated for this page. No comparison group was studied, so neither a difference from usual care nor its interval can be estimated. This page uses 10 percentage points as an analytical threshold for a comparative difference, but these data cannot test it. Lowered 1 level for risk of bias: no concurrent control; people enrolled while their disease was active, when some improvement is expected anyway; remission scores rest partly on patient-reported symptoms in people who knew their diet; and vitamin D and iron replacement, coaching and lifestyle guidance were given at the same time. Inconsistency not assessable with 1 study. Not lowered for indirectness: these are the people and the program the question names. Comparative imprecision remains unresolved; the small observed sample also limits precision. Publication bias not assessable. Low minus 1 is Very low, the lowest level, so further concerns cannot lower it.
Inflammatory bowel disease: quality of life on a 10 to 70 questionnaire at 11 weeks, before versus after the same supported program, without a concurrent control, same population	Not rated	This page’s own judgment. The same study’s quality of life report (Chandrasekaran, Groven, et al., 2019).	Not rated: only 4 of the 15 participants answered the last survey, and the paper reports the change among them both as P = 0.03 and as P = 0.07 depending on the test, which is too little to judge. Not rated does not mean no effect.
Inflammatory bowel disease: fecal calprotectin at 11 weeks, before versus after the same supported program, without a concurrent control, same population	Not rated	This page’s own judgment. The same study (Konijeti et al., 2017).	Not rated: only 6 participants gave stool samples at both times, all of them people in remission, and the fall was not statistically clear; with no comparison group, this is too little to judge. Not rated does not mean no effect.
Hashimoto’s thyroiditis: health-related quality of life on a 0 to 100 questionnaire after 10 weeks, before versus after an online AIP coaching program, without a concurrent control, women aged 20 to 45 with the condition and no other major conditions	Very low	GRADE, this page’s own judgment, from 1 single-group study read in full (Abbott et al., 2019): 17 enrolled, 16 completed.	Starts low as nonrandomized evidence. Estimate: all 8 subscales improved before versus after the supported program, for example general health from a median of 40 to 70, with a median within-person change of 28 points; the paper gives no interval for the change. A causal comparison with unchanged usual care cannot be estimated, because no concurrent comparison group was studied. This page uses 10 points on a 0 to 100 subscale as an analytical threshold for a comparative difference, but these data cannot test it. Lowered 1 level for risk of bias: no comparison group; outcomes self-reported by participants who knew their diet and were recruited through social media; the program combined the diet with coaching, a support group, lifestyle guidance and test-based individual advice; weight also fell. The intervention’s company co-founder was an author and another author was paid by that company, a possible route to bias in recruitment and reporting, not counted by itself. Inconsistency not assessable with 1 study. Not lowered for indirectness. Comparative imprecision remains unresolved: the threshold cannot be applied to a difference these data cannot estimate, and the within-person change has no reported interval; the small sample of 16 also limits precision. Publication bias not assessable. Low minus 1 is Very low.
Hashimoto’s thyroiditis: thyroid peroxidase (TPO) antibody level after 10 to 12 weeks, before versus after the diet programs, without a concurrent control, adults with the condition	Very low	GRADE, this page’s own judgment, from 2 single-group studies read in full: Abbott et al., 2019 (14 analyzed) and Ihnatowicz et al., 2023 (28 enrolled, 20 completed, number analyzed not stated).	Starts low as nonrandomized evidence. Threshold: a 20 percent relative change in the mean antibody level, this page’s judgment, as no published threshold for an important change was found. Estimates: 225 to 219 IU/mL in the first study, about 3 percent lower and not statistically clear; 210 to 294 IU/mL in the second, about 40 percent higher, P = 0.152 in the paper’s table, although its abstract calls the rise significant. An approximate 95 percent interval for the within-person change in the second study, calculated for this page from the reported P value assuming 20 complete pairs and the reported paired-t analysis, runs from about 34 IU/mL lower to 201 IU/mL higher. The 20 percent threshold is about 42 IU/mL at the reported baseline, so the interval includes no change and does not exclude an increase well above the threshold. It is an interval for the change within the study group, not for a difference from not changing the diet, which cannot be estimated without a concurrent control. Lowered 1 level for risk of bias: no concurrent comparison groups, 8 of 28 not completing the second study, and laboratory values taken before and after programs that also changed weight and, in one study, medication doses; a blood antibody measure is not itself biased by participants knowing their diet. Inconsistency: the 2 point estimates differ in direction, but neither is statistically clear, so no separate deduction. Not lowered for indirectness. Imprecision would also lower it: the conditional interval crosses both no change and the threshold. Publication bias not assessable. Low minus 1 is Very low, the lowest level.
Hashimoto’s thyroiditis: thyroid hormone levels (free T3 and free T4) after 10 to 12 weeks, before versus after the same diet programs, without a concurrent control, same population	Very low	GRADE, this page’s own judgment, from the same 2 studies, read in full (Abbott et al., 2019, 12 analyzed; Ihnatowicz et al., 2023, 20 of 28 completed).	Starts Low as uncontrolled nonrandomized evidence. Observed values, before versus after the diet programs without a concurrent control: no clear change in the first study, after excluding 2 women whose doses changed; in the second, mean free T3 fell from 3.31 to 2.88 pmol/L (P = 0.009) and mean free T4 from 1.36 to 1.20 ng/dL (P = 0.044), and thyroid-stimulating hormone fell from 3.72 to 2.69 mU/L without a statistically clear change (P = 0.416 in the paper’s table, although its abstract says it decreased). The reference ranges that paper reports are 2 to 4.4 pmol/L for free T3 and 0.93 to 1.7 ng/dL for free T4. A 2026 review reads these falls as a response to lower energy intake (Ruggeri et al., 2026). Serious risk of bias lowers certainty one level: no concurrent comparison group, incomplete follow-up, and concurrent treatment changes in the evidence body prevent attribution to the diet. The observed group means remained within the reference ranges reported by the studies; that does not establish clinical safety for individuals. This page found no validated clinically important change for these hormone outcomes. Conditional intervals for the within-person changes can be approximated from the reported paired-t P values if 20 complete pairs were analyzed, but the analysis denominator is not stated, and these are not intervals for final means or comparative diet effects. Imprecision and clinical importance therefore remain unresolved. The studies do not provide a secure basis to judge consistency of a clinically important effect. No indirectness deduction is made for the named population and intervention. Publication bias cannot be assessed. Low minus one reaches Very low. An individual can move outside a reference range even when a group mean does not, which is why the prescriber decides what monitoring each person needs.
Rheumatoid arthritis: self-rated disease activity on the 0 to 10 RAPID3 score after 8 weeks, the diet compared with each person’s own preceding 4 weeks on their usual diet, adults with rheumatoid arthritis on stable medication	Very low	GRADE, this page’s own judgment, from 1 single-group study with a usual-diet run-in, read in full (McNeill et al., 2026a): 11 enrolled, 9 completed.	A within-person comparison in a fixed order is nonrandomized, so it starts low. Threshold: a reduction of 1.2 points, the cutoff the study used for a meaningful response. Estimate: 1.52 points lower than during the usual-diet weeks, with a 95 percent interval from 0.14 to 2.90 points lower. Lowered 1 level for risk of bias: open label, a self-rated outcome, and the diet always followed the usual-diet weeks, so changes over time and expectation cannot be separated from the diet; the researcher who delivered the support also collected the outcomes, and a pandemic lockdown changed daily life during the study. Inconsistency not assessable with 1 study. Not lowered for indirectness, although about half started with low disease activity. Imprecision would also lower it: the interval includes reductions below and above the 1.2-point threshold, in 9 people. Publication bias not assessable. Low minus 1 is Very low.
Lupus, psoriasis, multiple sclerosis, celiac disease, type 1 diabetes, kidney disease and other autoimmune conditions: any outcome	Not rated	This page’s own judgment. Comparison: the diet against usual eating.	Not rated: the searches for this page found no published study of the autoimmune protocol in these conditions; a psoriasis and eczema study described by the promoter is unpublished, and a kidney disease trial was withdrawn. Not rated does not mean no effect or safe. The Wahls diet trials in multiple sclerosis are on the Paleo Diet page.
Any condition: the diet compared with another diet, usual eating or medication in a randomized trial	Not rated	This page’s own judgment.	Not rated: the searches for this page found no randomized trial of the diet. Not rated does not mean no effect.
Nutritional adequacy during the elimination phase	Not rated	This page’s own judgment. Single-group studies and reviews (Abbott et al., 2019; Ihnatowicz et al., 2023; Konijeti et al., 2017; Pardali et al., 2025).	Not rated: the searches found no study comparing nutrient status with and without the diet; one study recorded intake on menus its researchers planned, and calcium intake fell (Ihnatowicz et al., 2023). Not rated does not mean safe; calcium and iodine depend on which foods replace those removed.
Disordered eating during or after the diet	Not rated	This page’s own judgment.	Not rated: the searches for this page found no study that measured disordered eating in people following the diet. Not rated does not mean no effect.
Cardiovascular events, cancer and death	Not rated	This page’s own judgment. Comparison: the diet against usual eating, any population.	Not rated: the searches for this page found no study of these outcomes. Not rated does not mean no effect or safe.

The second table holds recommendations. The certainty of the evidence behind a recommendation is not the same as certainty about a treatment outcome, and a recommendation’s direction, for or against, is not a certainty level. None of these recommendations names the autoimmune protocol.

On a narrow screen, scroll the table sideways to see every column.

Recommendations and the certainty of the evidence behind them (not treatment-outcome certainty)

Recommendation	Evidence certainty, as published	Who made it, and on which scale	What the label covers
Rheumatoid arthritis: adherence to a formally defined diet other than a Mediterranean-style diet (recommended against)	Very low to moderate; conditional recommendation against	GRADE, published, 4-level scale: American College of Rheumatology guideline (England et al., 2023). Adults with rheumatoid arthritis, alongside disease-modifying drugs.	As published. The formally defined diets the panel evaluated are listed as anti-inflammatory, Mediterranean-style, ketogenic, paleo, gluten-free, vegetarian, vegan, intermittent fasting, elemental, elimination, raw foods and whole food plant-based; the autoimmune protocol is not named, so the label is not a rating of this diet. Read as the authors’ accepted manuscript; the recommendations and evidence labels match the published version.
Rheumatoid arthritis: adherence to a Mediterranean-style diet (recommended over no formally defined diet)	Low to moderate; conditional recommendation	GRADE, published, 4-level scale: England et al., 2023.	As published, for low to moderate certainty evidence of improvement in pain and no difference in physical function or disease activity. Shown here because it is the comparison the guideline favors; the evidence is on the Mediterranean Diet page.
Inflammatory bowel disease: a Mediterranean diet for all patients unless there is a contraindication	No evidence rating; best practice advice	American Gastroenterological Association clinical practice update (Hashash et al., 2024).	As published, an expert review that states it did not formally rate the quality of evidence. It also states that no diet has consistently been found to decrease the rate of flares in adults. Read as the abstract.
Inflammatory bowel disease with symptomatic strictures: fibrous, raw plant foods may not be tolerated; careful chewing and cooking to a softer consistency may help	No evidence rating; best practice advice	Hashash et al., 2024.	As published. Relevant to the hospitalization in the inflammatory bowel disease study of this diet. Read as the abstract.

How this archive talks about weight. This page reports what studies measured, including body weight, and does not treat weight change as a goal or as a measure of a diet’s success. Weight a person loses without meaning to can be a sign of a health problem, and where it is, the page names it as a reason to see a clinician. People are described the way the study described them.

Last reviewed: Reviewed and approved by James Peth, MS, MPH, PhD, on November 14, 2026, after a combined final review of the sixth batch of 5 archive pages, the repairs it asked for and a targeted recheck. Written October 21, 2026, and finished November 8, 2026.

What changed: First version. The judgments in the table are this page’s own, assigned from the evidence. Prices and program details in section 2 were rechecked on the companies’ and a bookseller’s pages on November 8, 2026; the U.S. News profile is described as it was read on October 21, 2026, because it refused an automated reader on November 8, 2026. Some sources could be read only as abstracts, and the page says so where each is used; none of them carries a rating.

After the combined final review on November 8, 2026, the rating rows were relabeled to say that no study had a concurrent comparison group, the reasoning for the thyroid hormone row was rebuilt, the thyroid medication guidance now says the client contacts the prescriber before a substantial change in eating, and statements about missing evidence were narrowed to what the searches for this page did not identify.

Next scheduled review: each year. Pages built on annual guidance are rechecked each year. The diet’s published research is small and growing, so new trials are checked first.

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Diet Reference Archive | One James

Prepared by James Peth, MS, MPH, PhD

© 2026–2027 One James. All rights reserved.

This page is for education and coaching practice. It is not medical or dietary advice.