The AIP Diet: Food List, How to Do It, and What Studies Found

The autoimmune protocol, usually shortened to AIP, is an elimination diet built on paleo principles. It removes a longer list of foods than standard paleo for a set period, then adds them back one at a time to find out which ones a person reacts to. This guide covers what the protocol removes, what it allows, how the phases work, and what the published pilot studies reported.

Key takeaways

• AIP was formalized by Sarah Ballantyne, PhD, in The Paleo Approach (2014). It is a temporary elimination and reintroduction process, not a permanent way of eating.
• The elimination phase removes grains, legumes, dairy, eggs, nuts, seeds, nightshades, refined sugar, alcohol, coffee, and processed food additives.
• Allowed foods are meat, organ meats, fish and shellfish, bone broth, most vegetables, fruit in moderation, fermented foods, coconut, olive oil, and fresh herbs.
• Three small uncontrolled pilot studies (IBD, Hashimoto's, Hashimoto's) reported fewer symptoms and better quality of life. None showed a drop in thyroid antibodies, and one recorded a rise.
• Anyone with a diagnosed condition or on medication should run the protocol with a practitioner who can watch labs and nutrient intake.

This article is for education only. It does not diagnose, treat, or replace medical care. Ivy Ham is a certified clinical herbalist, not a physician. Do not start or stop any medication based on what you read here. Elimination diets can change nutrient intake, body weight, and medication needs, and they are not appropriate for everyone, including people with a history of disordered eating, people who are pregnant or nursing, and children. Individual responses vary. If you are in crisis, contact your local emergency number or a crisis line.

What the autoimmune protocol is

Evidence: descriptive. This section summarizes the protocol as its author published it.

AIP starts from the paleo template (no grains, legumes, dairy, refined sugar, or seed oils) and removes additional foods that Ballantyne argued could irritate the gut lining or stimulate the immune system in susceptible people. The stated goal is to lower the load of dietary triggers while raising nutrient density, then use a structured reintroduction to learn which foods a person tolerates.¹

The protocol also includes lifestyle pieces that often get dropped in online summaries: sleep, stress management, daily movement, and time outdoors. The two published Hashimoto's pilots delivered AIP alongside health coaching, so the study results reflect the full package rather than food changes alone.⁴

People searching for a "Hashimoto diet" usually find AIP first. That is where the research attention has gone, and the reasons why are covered below in the section on what the studies found. Readers with thyroid concerns may also want the article on weight struggles and hypothyroidism.

Foods removed during the elimination phase

Evidence: descriptive. Listed as published in the protocol; the rationale for each exclusion is the author's.

The elimination phase removes every item on this list at the same time. Reading labels matters, since seed-based spices and nightshade spices show up in many prepared foods.

• Grains and pseudo-grains: wheat, rice, corn, oats, quinoa, buckwheat, amaranth, and anything made from them.
• Legumes: all types, including soy, peanuts, and pea protein.
• Dairy: milk, cheese, yogurt, butter, ghee, whey.
• Eggs: both the yolk and the white.
• Nuts and seeds: including nut and seed oils, nut flours, chia, flax, and seed spices such as cumin, coriander, fennel, mustard, black pepper, and nutmeg. Cocoa and coffee are seeds and are removed too.
• Nightshades: tomatoes, potatoes (sweet potatoes are fine), peppers of every kind, eggplant, goji berries, and nightshade spices such as paprika, cayenne, chili powder, and curry blends that contain them.
• Refined and processed sugars and sweeteners: including stevia and other non-caloric sweeteners.
• Alcohol.
• Food additives: emulsifiers, thickeners, and gums such as carrageenan and xanthan.
• NSAIDs: Ballantyne lists over-the-counter anti-inflammatories as a gut-lining irritant to discuss with a prescriber. This is a conversation with your doctor, not a dietary decision.

Two foods people ask about most often: honey and maple syrup are permitted in small amounts, and green beans are excluded during elimination because they are a legume, even though they are often tolerated well on reintroduction.¹

AIP food list: what you can eat

Evidence: descriptive. Food categories as published in the protocol.

• Meat and poultry: beef, lamb, bison, pork, chicken, turkey, game. Grass-fed and pasture-raised where possible.
• Organ meats: liver, heart, kidney. Ballantyne recommends organ meats several times a week for nutrient density.
• Fish and shellfish: wild-caught preferred, including oily fish for omega-3 fats.
• Bone broth and gelatin: a daily staple in most AIP meal plans.
• Vegetables: everything except nightshades. Leafy greens, root vegetables, squash, sweet potatoes, alliums, sea vegetables, and mushrooms all count. Cruciferous vegetables (cabbage, broccoli, kale) are allowed, though they contain compounds that can interfere with thyroid function when eaten raw in volume, so people with thyroid conditions often cook them and keep portions moderate.
• Fruit: permitted, with a guideline of roughly two servings a day during elimination.
• Fermented foods: sauerkraut, kimchi made without chili, coconut yogurt, kombucha.
• Fats: coconut oil, olive oil, avocado oil, avocado, animal fats such as tallow and lard. Seed oils are excluded, which lines up with the cooking oils guidance on this site.
• Herbs and non-seed spices: basil, cilantro, parsley, thyme, oregano, rosemary, ginger, turmeric, garlic, cinnamon, cloves, saffron, and sea salt.
• Sweeteners in small amounts: raw honey, maple syrup, dates, coconut sugar.
• Drinks: water, herbal teas, coconut water, bone broth. Green and black tea are permitted; coffee is not.

How to do the autoimmune protocol

Evidence: descriptive for the phase structure. Duration guidance comes from the protocol author and from the lengths used in the pilot studies.

Before starting, anyone taking medication (thyroid hormone, immunosuppressants, blood thinners, blood sugar drugs) should review the plan with a pharmacist or clinical herbalist, since a large diet change can shift how those drugs behave. Anyone with a diagnosed condition should have baseline labs on file so there is something to compare against.

Phase 1: elimination

Remove every food on the exclusion list at once. Ballantyne recommends a minimum of 30 days, and most people run it longer. The Scripps IBD pilot used a six-week elimination phase, and the Hashimoto's pilots ran ten and twelve weeks.^{2, 4, 5} The phase ends when symptoms have improved and stabilized, not on a fixed calendar date.

Two practical points from the pilot studies. First, calories matter. The Polish Hashimoto's study recorded weight loss across the group and concluded the participants were eating in a deficit, which is a common problem when a large number of familiar foods disappear at once.⁵ Plan meals around enough meat, fat, and starchy vegetables to stay fed. Second, the IBD pilot phased foods out over the first weeks rather than all on day one, which may be easier for people who cook for a household.²

Phase 2: reintroduction

Reintroduce one food at a time, in a set order, and wait before adding the next. Ballantyne's method: eat a small amount of the test food, wait 15 minutes, eat a larger amount, wait a few hours, then eat a full portion. Do not eat the food again for five to seven days while watching for any change in digestion, skin, joints, sleep, energy, or mood. If nothing changes, the food stays in. If something changes, the food goes back out and can be retested later.¹

The published order runs from the foods least likely to cause reactions to those most likely:

• Stage 1: egg yolks, legumes with edible pods (green beans, snap peas), fruit-based and seed-based spices, seed and nut oils, ghee from grass-fed butter.
• Stage 2: seeds, nuts (except cashews and pistachios), cocoa, egg whites, grass-fed butter, small amounts of alcohol.
• Stage 3: cashews and pistachios, eggplant, sweet peppers, paprika, coffee, grass-fed cream and fermented dairy.
• Stage 4: remaining nightshades (tomatoes, potatoes, chili peppers), gluten-free grains, white rice, other dairy, larger amounts of alcohol.

Most people finish reintroduction with a personal list of foods they keep out and a much longer list they eat freely. That personal list is the actual product of the protocol.

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What the studies found

Evidence: weak to moderate. Three small uncontrolled pilot studies and one follow-up analysis. No randomized controlled trial of AIP has been published.

Inflammatory bowel disease, Scripps Clinic, 2017. Eighteen adults with active Crohn's disease or ulcerative colitis enrolled; fifteen completed a six-week elimination phase followed by five weeks of maintenance. Eleven of the fifteen reached clinical remission by week six and stayed there through week eleven. Endoscopic scores improved in the subset who had follow-up scopes. There was no control group, and participants stayed on their existing medications.² A 2019 follow-up analysis of the same cohort reported improved patient-reported quality of life.³

Hashimoto's thyroiditis, Abbott et al., 2019. Seventeen women aged 20 to 45 with Hashimoto's enrolled in a ten-week program combining AIP with an online health coaching course; sixteen completed it. Quality-of-life scores rose, symptom burden fell, and hs-CRP (an inflammation marker) declined significantly. Thyroid function tests and thyroid antibodies did not change. The study was crowdfunded through Autoimmune Wellness, the company that sells the coaching program used in the trial; the lead author is that company's medical advisor and a co-author is its co-founder. Genova Diagnostics supplied lab testing.⁴

Hashimoto's thyroiditis, Warsaw, 2023. Twenty-eight euthyroid Hashimoto's patients followed AIP for twelve weeks with university funding and no commercial involvement. Reported symptoms decreased and thyroid volume on ultrasound fell. Free T3, free T4, and TSH all decreased but stayed within reference ranges. Thyroglobulin antibodies dropped slightly, while TPO antibodies rose significantly. Participants lost weight, which the authors read as a sign of unintended caloric restriction.⁵

Taken together, the pilots point in the same direction on symptoms and quality of life and give no support for the claim that AIP lowers thyroid antibodies. Small sample sizes, short durations, and the absence of control groups mean these results are a reason to study the diet properly, not a proof that it works.

Where AIP and the bioenergetic view disagree

Evidence: comparative. Both positions are presented as their authors stated them.

Readers of this site know the Ray Peat framework, and it conflicts with AIP on several points. Peat treated milk, cheese, ripe fruit, orange juice, and white rice as core foods and argued that starch-free, dairy-free diets tend to push people into a stress-hormone state that lowers thyroid output. AIP removes dairy and all grains during elimination and limits fruit. The Warsaw study's finding that TSH, free T3, and free T4 all fell during twelve weeks of AIP, alongside weight loss, is the kind of pattern Peat's writing would predict from under-eating.⁵

The two agree on more than the food lists suggest. Both remove seed oils and industrial additives, both favor gelatin and bone broth, both treat organ meats as nutrient-dense, and both are cautious about raw cruciferous vegetables. Someone running AIP with a Peat lens would keep starch high through sweet potato, cassava, plantain, and winter squash, keep fruit at the upper end of the allowance rather than the lower end, watch morning temperature and pulse for signs of a slowing metabolism, and make dairy the first reintroduction rather than the last. The seven-day bioenergetic meal plan shows what that style of eating looks like in practice.

Cautions on record for elimination diets

Evidence: moderate. Drawn from the pilot study limitations and general clinical nutrition literature on restrictive diets.

The safety questions raised in the AIP literature are about restriction rather than any single food. Unplanned calorie deficits appeared in the Warsaw cohort. Removing grains, legumes, dairy, eggs, nuts, and seeds together takes out common sources of calcium, iodine, B vitamins, fiber, and calories, and the protocol depends on organ meats, bone broth, seafood, and large vegetable portions to fill those gaps. People who skip the organ meats and seafood are the ones most likely to run short. Clinicians also note that long stays in the elimination phase, well past the point where symptoms have settled, carry the nutritional cost without adding benefit, and that people with a history of disordered eating should be cautious with any protocol built around removing foods. For people on thyroid medication, changes in weight and diet can shift dosing needs, which is a reason to keep a prescriber informed. Readers interested in the gut-lining rationale behind AIP can find it covered in the article on intestinal permeability.

Frequently asked questions

Evidence: descriptive. Answers reflect the protocol as published.

What does AIP stand for?

Autoimmune protocol, sometimes called the autoimmune paleo diet. Both names refer to the same elimination and reintroduction process.

How long does the AIP elimination phase last?

Ballantyne recommends at least 30 days. The published pilots ran six, ten, and twelve weeks. The phase ends when symptoms have stabilized, and reintroduction begins after that.

Are eggs allowed on AIP?

No, not during elimination. Egg yolks are the first food reintroduced in stage 1, and egg whites come in stage 2.

Is coffee AIP compliant?

No. Coffee is a seed and is removed during elimination. It is reintroduced in stage 3. Green and black tea are permitted throughout.

Is rice AIP compliant?

No. All grains are removed during elimination. White rice is among the last foods reintroduced, in stage 4.

Are sweet potatoes a nightshade?

No. Sweet potatoes belong to the morning glory family and are allowed. White potatoes are nightshades and are removed.

Is honey allowed on AIP?

Yes, in small amounts, along with maple syrup, dates, and coconut sugar. Refined sugar and non-caloric sweeteners are removed.

Does AIP lower Hashimoto's antibodies?

The two published Hashimoto's pilot studies did not find a reduction. One found no change in antibodies; the other found thyroglobulin antibodies dropped slightly while TPO antibodies rose. Symptoms and quality-of-life scores improved in both.

Is AIP the same as paleo?

AIP starts from paleo and removes more: eggs, nuts, seeds, nightshades, seed and nightshade spices, coffee, cocoa, and alcohol. Standard paleo allows all of those.

Sources

1. Ballantyne S. The Paleo Approach: Reverse Autoimmune Disease and Heal Your Body. Victory Belt Publishing; 2014. Primary source for the protocol's exclusion list, food list, and reintroduction stages. The author sells books and courses built on the protocol.
2. Konijeti GG, Kim N, Lewis JD, et al. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017;23(11):2054-2060. doi:10.1097/MIB.0000000000001221. Sponsored by Scripps Health; the coaching program used was supplied by Autoimmune Wellness.
3. Chandrasekaran A, Groven S, Lewis JD, et al. An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease. Crohns Colitis 360. 2019;1(3):otz019. doi:10.1093/crocol/otz019.
4. Abbott RD, Sadowski A, Alt AG. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto's Thyroiditis. Cureus. 2019;11(4):e4556. doi:10.7759/cureus.4556. Crowdfunded through Autoimmune Wellness; Abbott is the company's medical advisor and Alt is its co-founder. Lab testing was provided by Genova Diagnostics.
5. Ihnatowicz P, Gębski J, Drywień ME. Effects of Autoimmune Protocol (AIP) diet on changes in thyroid parameters in Hashimoto's disease. Ann Agric Environ Med. 2023;30(3):513-521. doi:10.26444/aaem/166263. Funded by the Polish Ministry of Education and Science through the Warsaw University of Life Sciences; no commercial funding reported.