What Is the Autoimmune Protocol (AIP) Diet?

The Autoimmune Protocol (AIP) diet is an elimination-style dietary approach designed to reduce inflammation, heal the gut lining, and identify food triggers in people with autoimmune conditions. Developed as an extension of the Paleo diet, AIP removes foods most commonly associated with immune activation and intestinal permeability, then systematically reintroduces them to identify individual sensitivities.

Research published in Inflammatory Bowel Diseases (2017) demonstrated that an AIP diet led to clinical remission in 73% of participants with inflammatory bowel disease after just six weeks, suggesting significant potential for autoimmune-driven pain conditions.¹

Nutrition Facts: AIP Diet at a Glance

Type: Elimination and reintroduction protocol
Duration: 30–90 day elimination phase, followed by gradual reintroduction
Foods allowed: Vegetables (except nightshades), quality meats, seafood, fermented foods, bone broth, healthy fats
Foods removed: Grains, dairy, eggs, nuts, seeds, nightshades, legumes, refined sugars, alcohol, coffee
Nutrient focus: Nutrient density, organ meats, seafood, colorful vegetables
Research status: Emerging evidence supports efficacy for IBD, Hashimoto’s, and rheumatoid arthritis

How AIP Addresses Autoimmune Pain

Autoimmune conditions such as rheumatoid arthritis, lupus, multiple sclerosis, and Hashimoto’s thyroiditis involve the immune system attacking the body’s own tissues, often causing chronic pain, fatigue, and widespread inflammation. The AIP diet targets several mechanisms involved in this process:

Intestinal permeability (“leaky gut”): Certain food compounds (gluten, lectins, saponins) may increase gut permeability, allowing immune-reactive molecules to enter the bloodstream and trigger systemic inflammation²
Molecular mimicry: Some food proteins structurally resemble human tissues, potentially confusing the immune system and driving autoimmune attacks
Gut microbiome modulation: AIP emphasizes prebiotic-rich vegetables and fermented foods that support a diverse, anti-inflammatory gut microbiome
Nutrient repletion: By focusing on organ meats, seafood, and colorful vegetables, AIP provides nutrients commonly deficient in autoimmune patients (vitamin D, zinc, selenium, omega-3 fatty acids)
Immune calming: Removing common inflammatory triggers allows the immune system to down-regulate its hyperactive response

The Elimination Phase

The elimination phase typically lasts 30 to 90 days. During this period, you remove all potentially inflammatory foods while maximizing nutrient intake:

Foods to Enjoy

All vegetables except nightshades (sweet potatoes, leafy greens, cruciferous vegetables, squash, beets, carrots)
Quality proteins: grass-fed meats, wild-caught fish, organ meats, poultry
Healthy fats: olive oil, coconut oil, avocado oil, animal fats
Fruits in moderation (berries, citrus, apples, pears)
Fermented foods: sauerkraut, kimchi, kombucha, coconut yogurt
Bone broth and collagen-rich foods
Fresh herbs: basil, oregano, thyme, rosemary, mint

Foods to Remove

All grains (wheat, rice, oats, corn)
Dairy products (milk, cheese, yogurt, butter)
Eggs
Nuts and seeds (including cocoa and coffee)
Nightshade vegetables (tomatoes, peppers, eggplant, potatoes)
Legumes (beans, lentils, peanuts, soy)
Refined sugars and artificial sweeteners
Alcohol and NSAIDs (which damage gut lining)

The Reintroduction Phase

After the elimination phase, foods are reintroduced one at a time over 5–7 day intervals while carefully monitoring symptoms. This structured approach helps identify which specific foods trigger your symptoms:

Stage 1 (least likely to cause reactions): Egg yolks, legumes with edible pods (green beans), seed-based spices, fruit-based spices, seed and nut oils
Stage 2: Seeds, nuts, cocoa/chocolate, egg whites, ghee, alcohol in small amounts
Stage 3: Nightshades, coffee, dairy (grass-fed butter, then cream, then fermented dairy)
Stage 4 (most likely to cause reactions): Gluten-free grains, gluten-containing grains, whole eggs, dairy (milk, cheese)

A 2019 study in Cureus found that participants with Hashimoto’s thyroiditis who completed the AIP protocol experienced significant improvements in quality of life and a reduction in inflammatory markers, even before any food reintroductions.³

Research Evidence for Autoimmune Pain

While AIP research is still emerging, several studies have shown promising results:

Inflammatory bowel disease: A 2017 study in Inflammatory Bowel Diseases found that 73% of participants achieved clinical remission after 6 weeks on AIP, with 16 of 17 patients maintaining remission through the maintenance phase¹
Hashimoto’s thyroiditis: A 2019 pilot study showed significant improvement in quality of life scores and reduction in inflammation markers, including high-sensitivity C-reactive protein³
Rheumatoid arthritis: Observational data suggests that AIP may reduce disease activity scores, though randomized controlled trials are still needed
Multiple sclerosis: Dr. Terry Wahls developed a modified AIP approach (the Wahls Protocol) that showed improvements in fatigue and quality of life in a pilot study published in the Journal of Alternative and Complementary Medicine (2014)⁴

Practical Tips for Starting AIP

Plan ahead: Batch cook compliant meals before starting the elimination phase to reduce overwhelm
Stock your kitchen: Remove non-compliant foods and stock up on AIP-friendly staples
Keep a symptom journal: Track pain levels, energy, digestion, mood, and sleep quality daily
Focus on what you can eat: AIP includes a wide variety of meats, fish, vegetables, fruits, and healthy fats
Manage the social aspect: Prepare responses for social situations and bring compliant dishes to gatherings
Work with a practitioner: A registered dietitian experienced with AIP can help ensure nutritional adequacy
Be patient: Healing takes time; some people notice improvements within weeks, while others require the full 90 days

Potential Challenges and Considerations

The AIP diet is restrictive, and certain challenges should be anticipated:

Nutrient adequacy: Without grains, dairy, and eggs, careful planning is needed to meet calcium, fiber, and certain B vitamin needs
Cost: Quality meats, organ meats, and wild-caught seafood can be expensive; consider frozen options and less popular cuts
Social isolation: Eating out and social meals become more challenging on AIP
Die-off symptoms: Some people experience temporary worsening of symptoms in the first 1–2 weeks as the body adjusts
Not suitable for everyone: People with eating disorders, severe caloric restriction histories, or certain medical conditions should consult their provider before starting

Frequently Asked Questions

How long should I stay on the elimination phase?

Most practitioners recommend 30–90 days, with 60 days being a common recommendation. Stay on the elimination phase until you notice meaningful symptom improvement or reach 90 days, whichever comes first.

Can I do AIP while taking immunosuppressant medications?

Yes, AIP is a dietary approach that complements medical treatment. Never stop or reduce medications without your doctor’s guidance. Many people use AIP alongside conventional treatment.

Is AIP safe long-term?

The full elimination phase is not intended for long-term use. The goal is to identify triggers and reintroduce as many foods as tolerated. A personalized long-term diet should include the widest variety possible while avoiding identified triggers.

Will AIP cure my autoimmune condition?

AIP is not a cure but may help manage symptoms and reduce flares. Autoimmune conditions are chronic, and AIP is one tool in a comprehensive management strategy.

What if I don’t see improvement after 90 days?

If there is no improvement, other factors such as stress, sleep, infections, environmental toxins, or medication needs should be explored with your healthcare team.

Related Resources

References

Konijeti GG, et al. Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflamm Bowel Dis. 2017;23(11):2054–2060.
Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol. 2012;42(1):71–78.
Abbott RD, et al. Efficacy of the autoimmune protocol diet as part of a multi-disciplinary, supported lifestyle intervention for Hashimoto’s thyroiditis. Cureus. 2019;11(4):e4556.
Wahls TL, et al. A randomized trial of dietary improvement for adults with major depressive disorder and the Wahls elimination diet. J Altern Complement Med. 2014;20(5):A24.
Chandrasekaran A, et al. An autoimmune protocol diet improves patient-reported quality of life in inflammatory bowel disease. Crohn’s Colitis 360. 2019;1(3):otz019.
Ballantyne S. The Paleo Approach: Reverse Autoimmune Disease and Heal Your Body. Victory Belt Publishing; 2014.

AIP Diet for Autoimmune Pain