The Autoimmune Protocol Diet (AIP Diet) : Does It Help?

By Amy Burkhart, MD, RD

The autoimmune protocol diet, also known as the AIP diet, has gained attention as autoimmune diseases become more common. While most treatments for autoimmune conditions rely on medications that suppress or alter the immune system, many people want alternative or additional treatment options.

Could the autoimmune protocol diet be a helpful addition to current treatments? What does science say? And do people living with autoimmune conditions report real benefits from following an AIP diet?

The AIP diet eliminates foods that may cause symptoms or increase inflammation.

The AIP diet, short for Autoimmune Protocol diet, is a way of eating that helps people with autoimmune conditions feel better by reducing symptoms and inflammation. It works by removing foods that can trigger flare-ups and focusing on nutrient-rich options that support gut health. Since the gut is closely linked to the immune system, keeping it healthy can help the immune system function more effectively and stay balanced.

The specific definition of the Autoimmune Protocol Diet varies depending on the source, but in general:

• ✅ AIP Diet – Foods Allowed

  • Vegetables (except nightshades):

    • Leafy greens, carrots, beets, broccoli, cauliflower, sweet potatoes, etc.

  • Fruit (in moderation):

    • Berries, apples, bananas, pears, etc.

  • Meats & Fish:

    • Grass-fed beef, pasture-raised poultry, wild-caught fish, organ meats

  • Shellfish

  • Bone Broth

  • Healthy Fats:

    • Coconut oil, olive oil, avocado oil, animal fats (e.g., lard, tallow)

  • Fermented Foods (without added sugar):

    • Sauerkraut, kimchi (without nightshades), kombucha

  • Herbs & Spices (non-seed-based):

    • Basil, thyme, oregano, garlic, ginger, turmeric, etc.

  • Coconut products:

    • Coconut milk, flour, shredded coconut (additive-free)

  • AIP-compliant flours:

    • Cassava flour, arrowroot flour, tigernut flour

  • Green tea & herbal teas (non-seed based)

• 🚫 AIP Diet – Foods to Avoid

  • Grains:

    • Wheat, rice, oats, corn, quinoa, etc.

  • Legumes:

    • Beans, lentils, soy, peanuts, chickpeas

  • Dairy (even fermented)

  • Nightshade vegetables:

    • Tomatoes, potatoes (white), eggplants, peppers, paprika

  • Eggs

  • Nuts & Seeds:

    • Almonds, walnuts, chia, flax, sunflower, sesame, etc.

  • Seed-based spices:

    • Mustard, cumin, coriander, fennel, etc.

  • Processed foods:

    • Anything with preservatives, additives, refined sugars

  • Refined/industrial oils:

    • Canola oil, soybean oil, vegetable oil

  • Coffee & Alcohol

  • Chocolate & Cocoa

  • Sweeteners:

    • Refined sugar, stevia, honey (only in reintroduction phase)

An autoimmune condition arises when the body’s immune system mistakenly attacks its own healthy cells.

When a person’s body fails to distinguish between self and foreign invaders, this misdirected immune response can lead to chronic inflammation, tissue damage, and various health complications.

Example: Type 1 Diabetes

Type 1 diabetes is an example of a well known autoimmune disorder:

• Immune System Attack: The immune system targets and destroys insulin-producing beta cells in the pancreas.

• Insulin Dependency: This destruction results in little to no insulin production, necessitating lifelong insulin therapy through injections or pumps.

• Onset and Management: While often diagnosed in children and young adults, type 1 diabetes can develop at any age. Managing the condition involves regular blood glucose monitoring and insulin administration.

Other Common Autoimmune Conditions

There are over 80 recognized autoimmune disorders. Some of the most prevalent include: 

• Celiac Disease

• Crohn’s Disease

• Hashimoto’s Thyroiditis

• Lupus (Systemic Lupus Erythematosus)

• Multiple Sclerosis (MS)

• Rheumatoid Arthritis

• Sjögren’s Syndrome

• Transverse Myelitis

• Ulcerative Colitis

These conditions can affect various organs and systems, leading to a wide range of symptoms and complications.

Increasing Diagnosis Rates

The rise in autoimmune disease diagnoses cannot be solely attributed to genetics. While genetic predisposition plays a role, environmental factors are increasingly recognized as significant contributors. Diet, infections, and other environmental exposures may trigger or exacerbate autoimmune responses in genetically susceptible individuals.

While genetics can increase our susceptibility to autoimmune diseases, diet plays a significant role in influencing our overall health and immune system function.

Celiac Disease: A Diet-Specific Autoimmune Disorder

Celiac disease is an autoimmune disorder that is managed exclusively through dietary changes:

• Gluten-Free Diet: The primary treatment involves eliminating gluten from the diet.

• Impact on the Microbiome: Adopting a gluten-free diet has been shown to positively alter the gut microbiome—the community of bacteria in our intestines.

The Microbiome’s Influence on the Immune System

The gut microbiome plays a crucial role in regulating the immune system:

• Immune Regulation: A balanced microbiome helps maintain immune system balance and function.

• Dietary Impact: What we eat can significantly affect the diversity and health of our gut bacteria.

Diet and Autoimmune Diseases: Emerging Research

Scientists are increasingly exploring how diet can influence autoimmune diseases:

• Diverse Gut Bacteria: Studies suggest that a diverse and healthy gut microbiome can positively affect individuals with autoimmune diseases.

• Dietary Changes: Modifying one’s diet in specific ways can enhance microbial diversity in the gut.

The Autoimmune Protocol (AIP) Diet

The AIP diet is designed to support gut health and modulate the immune system:

• Focus on Nutrient-Dense Foods: The diet emphasizes whole, unprocessed foods rich in nutrients.

• Elimination of Potential Triggers: It involves removing foods that may cause inflammation or immune system activation.

• Goal: The primary aim is to improve gut health and reduce autoimmune symptoms by enhancing the diversity of gut bacteria.

While genetic factors, stress, and sleep also contribute to autoimmune diseases, diet plays a pivotal role in managing and potentially mitigating these conditions. By focusing on gut health and making informed dietary choices, individuals may positively influence their immune system and overall well-being.

The Autoimmune Protocol (AIP) Diet was developed around 20 years ago to help manage autoimmune conditions by reducing inflammation and promoting gut health.

Dr. Loren Cordain’s Contribution

Dr. Loren Cordain, a professor at the University of Colorado, is credited with laying the foundation for the AIP diet. He proposed that certain foods could trigger inflammation in individuals with autoimmune diseases.

Immunonutrition is the use of diet manipulation to regulate the immune system.

While it may seem intuitive that diet matters, scientific evidence is beginning to reveal how it may improve quality of life and reduce disease symptoms. The AIP is one diet used to determine, through elimination and personalization, how diet may help autoimmune conditions. The AIP diet and the following autoimmune conditions have been studied so far. In addition, a 2024 study did an overview report on the use of the AIP diet in autoimmune disease.

The AIP diet may help reduce inflammation, which is especially important for autoimmune conditions.

In 2017, a small study involving 15 people looked at how the Autoimmune Protocol (AIP) diet might help those with inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis.

Participants first followed a 6-week elimination phase, gradually removing foods not allowed on the AIP diet. They then continued with the full diet for another 5 weeks.

The results were encouraging: 73% of participants went into remission after the initial 6 weeks and remained in remission while staying on the diet. Follow-up tests, including endoscopies, showed reduced inflammation in the gut.

After 10 weeks, the AIP diet combined with lifestyle changes led to noticeable improvements in quality of life, reduced disease symptoms, and lower blood levels of inflammation.

A 2019 study used the AIP diet, in conjunction with lifestyle changes, to assess the effect on people with Hashimoto’s thyroid disease.

A 2023 report showed that 12 weeks on an AIP diet decreased malaise and improved some of the thyroid blood tests. These studies pave the way for larger studies looking at this diet and factors that may help the 14 million people (in the US alone) with this common autoimmune disorder.

Lifestyle changes helped people with multiple sclerosis (MS) feel better and have fewer symptoms.

In 2015, a study found that people with multiple sclerosis (MS), a disease that affects the nervous system, felt better after making dietary changes similar to the Autoimmune Protocol (AIP) diet.

The diet used in the study was developed by Dr. Terry Wahls, a physician who has MS herself. When conventional treatments didn’t work for her, she adopted a version of the paleo diet, similar to AIP, along with other lifestyle changes.

Dr. Wahls experienced a dramatic improvement; she went from using a wheelchair to riding a bike again. However, her recovery wasn’t due to diet alone. Her approach also included daily stretching, supplements, and stress reduction, making it difficult to know how much of the benefit came from food specifically.

Although the study was small, the results are promising. More research is needed to better understand how diet and lifestyle changes may help people with MS.

Dr. Alessio Fasano discovered zonulin, the protein that determines how leaky (permeable) the gut is.

Gut permeability is increased in people with autoimmune conditions and can lead to more inflammation, symptoms, and health problems. 

Although Dr. Fasano isn’t studying the AIP diet specifically, he’s extensively researched gluten, autoimmune diseases, and gut health. He discovered zonulin, a marker of increased gut permeability, often called “leaky gut.“. For some people, gluten may increase gut permeability and zonulin levels, highlighting a way that diet can impact autoimmune disease.

The AIP diet eliminates many common food groups that we enjoy for comfort, celebrations, and convenience.

Changing the way you eat—especially if it means cutting out a lot of foods—can be tough emotionally and socially, especially over time.

Starting a diet like AIP (Autoimmune Protocol) can also be costly, and unless you use a meal delivery service, you’ll likely need to cook most of your meals yourself. That can feel overwhelming, especially if you’re already dealing with fatigue from an autoimmune condition. Even small changes in your diet can feel like a big effort.

It’s a major lifestyle shift, and that can feel like a lot to take on. But if changing your diet has the potential to improve your health and quality of life, it might be worth trying—just be sure you’re ready for the challenge.

Main:

• Homemade Chicken Sausage Patties (ground chicken, garlic powder, onion powder, sage, sea salt)

• Fresh Blueberries (½ cup)

Extras:

• Sautéed Kale in Olive Oil (lightly wilted with a touch of sea salt)

• Herbal Tea

Prep Tip:
Make the sausage patties in batches and freeze them for quick breakfasts.

Main:

• Spaghetti Squash with AIP-Seasoned Ground Beef
  (Season with garlic, onion, oregano, and parsley. Serve on a bed of spaghetti squash strands.)

Side Salad:

• Mixed Greens (arugula, spinach, romaine)

• Sliced Cucumber, Carrot Ribbons, and Avocado

• Dressing: Olive oil + lemon juice + pinch of sea salt

Optional Add-On:

• Sprinkle with crushed seaweed for a salty, mineral-rich boost.

Main:

• Oven-Baked Salmon Filet (seasoned with sea salt, garlic powder, dill, and lemon slices)

• Sweet Potato Wedges (baked in coconut oil, sprinkled with rosemary)

Sides:

• Sautéed Mushrooms in coconut oil (add chopped garlic and fresh thyme if desired)

• Steamed Broccoli with a drizzle of olive oil

• Homemade or Store-Bought AIP-Approved Plantain Chips (check for no seed oils or non-AIP spices)

• Coconut Yogurt (unsweetened) with cinnamon and a few sliced strawberries

• Bone Broth (great for gut healing and satisfying between meals)

• Filtered Water

• Herbal teas

• Coconut water (in moderation, and unsweetened)

A few of the following AIP meal delivery services might be available near you.

While many restaurants may have a hard time providing you with compliant AIP meals, AIP meal delivery kits or services may be an option.

• Paleo On The Go
• Pete’s Real Food
• The Good Kitchen
• Urban AIP
• Wild Zora

There’s still a lot we don’t know about what causes autoimmune conditions, but one thing we can control is our diet.

Other lifestyle factors, such as getting enough sleep, managing stress, staying active, and keeping your vitamin D levels in a healthy range, also play a role. All of these things can affect inflammation, which is especially important when dealing with autoimmune issues.

Research now shows that food can influence autoimmune conditions. Early studies on the AIP (Autoimmune Protocol) diet have shown promising results. This diet has been found to reduce inflammation, improve symptoms, and boost energy levels.

The AIP diet isn’t easy, and it might not be right for everyone. But if you’re struggling with an autoimmune condition, it could be the solution you’ve been looking for.

• Efficacy Of The Autoimmune Protocol Diet For Inflammatory Bowel Disease
• Efficacy Of The Autoimmune Diet For Hashimoto’s Thyroid Disease
• The Autoimmune Protocol Diet And Effect On Quality Of Life In Inflammatory Bowel Disease
• The Autoimmune Protocol Diet And Its Effect On Gene Expression In Inflammatory Bowel Disease