The Autoimmune Protocol (AIP): A Guide by a Registered Dietitian

The Autoimmune Protocol (AIP) is a strategic dietary approach designed to help individuals with autoimmune diseases identify and eliminate foods that may be causing inflammation and other symptoms. Like other elimination diets, AIP focuses on removing potential inflammatory triggers and reintroducing foods gradually to understand how each affects your body. AIP is most commonly used by those with autoimmune disorders such as rheumatoid arthritis, psoriasis, Hashimoto’s thyroiditis, and inflammatory bowel diseases (IBD).

What Is the AIP Diet?

At its core, AIP is both a diet and a lifestyle change. The diet emphasizes nutrient-dense foods that support gut health, hormone regulation, and immune system balance while eliminating foods known to potentially cause inflammation. AIP is somewhat similar to the paleo diet but is more restrictive, focusing on foods that promote healing. The diet has three main phases: elimination, reintroduction, and maintenance. 

Why Consider the AIP Diet?

Autoimmune diseases are often associated with inflammation, which can manifest as fatigue, headaches, digestive issues, joint pain, skin changes, and more. Some research suggests that this inflammation might be triggered by a “leaky gut,” where the intestinal lining becomes permeable, allowing unwanted substances to enter the bloodstream and provoke an immune response.

The AIP diet aims to reduce inflammation and restore gut health by eliminating foods that might be causing immune system dysregulation. By focusing on anti-inflammatory, nutrient-dense foods, you can potentially alleviate symptoms and improve your overall quality of life.

Understanding Autoimmunity and the Role of AIP

Autoimmune diseases occur when the body’s immune system mistakenly attacks its own proteins, cells, and tissues. There are over a hundred confirmed autoimmune diseases, including rheumatoid arthritis, Hashimoto’s thyroiditis, and psoriasis. Although the exact cause of autoimmunity remains unclear, research suggests that factors like genetic predisposition, gut health, and environmental influences play a critical role.

Interestingly, about 30% of people have measurable levels of autoantibodies (antibodies that attack native proteins) in their blood at any given time. While the immune system usually has mechanisms to suppress such autoimmunity, these failsafes sometimes break down, leading to an autoimmune response and subsequent disease. The AIP diet is designed to mitigate these responses by focusing on foods that nourish the body and support immune regulation.

The Three Phases of the AIP Diet

Phase 1: Elimination

The elimination phase is the most restrictive and can last anywhere from 4-6 weeks to several months. During this phase, you remove foods known to potentially trigger inflammation or upset the gut microbiome. These include:

• Grains (gluten-containing and gluten-free)
• Legumes (beans, peas, lentils)
• Nightshade vegetables (tomatoes, potatoes, peppers)
• Dairy products
• Processed foods and refined sugars
• Eggs
• Nuts and seeds
• Coffee and alcohol
• Food additives like artificial sweeteners

While this may seem overwhelming, it’s important to focus on what you can eat. Nutrient-rich foods such as fresh vegetables (except nightshades), fruits, grass-fed meats, organ meats, fish, and healthy fats like olive oil are staples. The goal of this phase is to alleviate symptoms and start the healing process.

Phase 2: Reintroduction

After you’ve noticed significant improvement in your symptoms during the elimination phase, you can begin the reintroduction phase. This process helps identify specific foods that may be contributing to your symptoms.

Reintroduce foods one at a time, waiting 5-7 days between each new food. Start with a small portion of the food and monitor your body’s reaction. If no symptoms arise, gradually increase the portion size. If you experience any symptoms (digestive distress, headaches, skin changes), stop consuming that food and avoid it going forward. Reintroducing foods slowly allows you to understand which foods your body can tolerate and which you should avoid.

Phase 3: Maintenance

The maintenance phase is a personalized diet based on the findings from the first two phases. This phase emphasizes diversity in food choices while avoiding any foods that you found to be problematic. It is a long-term approach to managing your autoimmune condition through a focus on nutrient-dense foods and a balanced lifestyle. During this phase, it’s also encouraged to be flexible—occasionally eating non-AIP foods in moderation if they don’t cause significant symptoms.

Foods to Avoid and Include on the AIP Diet

Avoid:

• Grains: Rice, oats, wheat, corn, and products made with these ingredients.
• Legumes: Beans, lentils, soy, and products made from them.
• Nightshades: Tomatoes, peppers, eggplants, and spices like paprika.
• Dairy: Milk, cheese, butter, and other dairy-based products.
• Processed Foods: Packaged snacks, processed meats, refined sugars, and artificial additives.

Include:

• Vegetables: Non-nightshade varieties like spinach, zucchini, and sweet potatoes.
• Fruits: Apples, berries, oranges, mangoes.
• Minimally Processed Meats: Grass-fed beef, fish, organ meats, and poultry.
• Healthy Fats: Olive oil, avocado oil, and coconut oil.
• Herbs and Spices: Ginger, garlic, oregano, and salt.

Lifestyle: The Essential Component of AIP

AIP is not just about food; it’s a holistic lifestyle approach. Adequate sleep, stress management, regular physical activity, and spending time in nature are crucial components. Chronic stress and poor sleep can increase intestinal permeability (“leaky gut”), disrupt gut bacteria, and trigger inflammation. Therefore, incorporating relaxation techniques, maintaining a regular sleep schedule, and engaging in moderate exercise are vital for maximizing the benefits of the AIP diet.

The Science Behind AIP: Evidence of Effectiveness

Several clinical trials support the effectiveness of the AIP diet. In a 2017 study, patients with inflammatory bowel disease (IBD) followed the AIP diet for six weeks and achieved a clinical remission rate of 73%. Another 2019 study showed significant improvements in quality of life and reductions in systemic inflammation in women with Hashimoto’s thyroiditis. These studies highlight AIP’s potential to be a powerful tool in managing autoimmune conditions, although it’s important to recognize that individual responses can vary.

1. Konijeti, Gauree G., et al. “Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease.” Inflammatory Bowel Diseases, vol. 23, no. 11, 2017, pp. 2054-2060.
2. Abbott, Roberta D., Angela Sadowski, and Angie Alt. “The Autoimmune Protocol Diet Modifies Quality of Life in Women with Hashimoto’s Thyroiditis: A Pilot Study.” Cureus, vol. 11, no. 4, 2019, e4556.

Take-Home Messages:

1. A Holistic Approach: AIP focuses on more than just diet. It integrates nutrient-dense eating with lifestyle changes, such as stress management and sleep, to create an environment that supports immune regulation and healing.
2. Personalized Healing: AIP is a journey of self-discovery. By carefully eliminating and reintroducing foods, you gain insights into what works best for your body. It’s not a one-size-fits-all diet but a tailored strategy based on your unique responses.
3. Lifestyle Matters: Managing autoimmune conditions isn’t just about food. Regular sleep, stress management, and moderate physical activity are key factors in reducing inflammation and supporting overall health.
4. Nutrient Density Over Restriction: While AIP has an elimination phase, its primary goal is to flood your body with nutrient-rich foods. Foods like organ meats, fish, and a variety of vegetables are essential for providing the building blocks your body needs to heal.
5. Not a Life Sentence: The AIP diet is not meant to be a permanent restriction. It is a method to identify and eliminate triggers, allowing for more dietary flexibility as you progress to the maintenance phase.

In summary, the AIP diet is a comprehensive approach designed to address the underlying factors that contribute to autoimmune diseases. By focusing on nutrient density, gut health, hormone regulation, and immune function, it offers a pathway to better health and quality of life.