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The AIP Diet: An Effective Approach to Managing Autoimmune Conditions

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The AIP Diet: An Effective Approach to Managing Autoimmune Conditions

Autoimmune diseases affect approximately one in ten individuals, and their prevalence continues to increase over time. The chronic and debilitating nature of autoimmune diseases imposes a significant burden on patients, impacting not only their physical and emotional well-being but also leading to elevated medical costs and a diminished quality of life, thus affecting not only the individuals themselves but also placing strain on their families (5).

The intricate nature of autoimmune diseases underscores the need for a multifaceted and comprehensive approach to treatment. Research has increasingly linked diet to autoimmune disease severity, prompting a shift toward a food-as-medicine approach in the management of these conditions. The Autoimmune Protocol (AIP) diet, made popular by Dr. Loren Cordain in the early 2000s, has gained attention for its ability to mitigate inflammation and alleviate autoimmune-related symptoms. This article serves as an overview of the AIP diet for autoimmune management. 


What Are Autoimmune Conditions?

Autoimmune diseases represent a group of conditions wherein the immune system mistakenly targets and attacks its own tissues. The intricate balance of the immune system, particularly the regulatory T cells responsible for maintaining self-tolerance, can be disrupted, contributing to the onset of autoimmune conditions. This loss of self-tolerance results in chronic inflammation and damage to various organs and systems. The factors contributing to the development and severity of autoimmunity are multifaceted, involving a complex interplay of genetic predisposition, environmental triggers, and immune system dysregulation.

While the genetic component undeniably holds substantial influence as a risk factor for autoimmune disease, the interplay between environmental triggers and susceptible genotypes ultimately determines the manifestation and progression of autoimmunity. Infections, exposure to toxins, stress, dietary habits, and use of certain medications are examples of factors that can trigger autoimmunity in genetically predisposed individuals. (6

Commonly shared symptoms of autoimmune diseases encompass fatigue, joint pain, skin problems, digestive symptoms, recurring fever, and swollen glands. However, the manifestations can vary widely depending on the specific organs or tissues affected. There are over 80 types of autoimmune diseases, collectively affecting more than 24 million people in the United States. Examples of autoimmune diseases include rheumatoid arthritis, lupus, type 1 diabetes, Hashimoto's thyroiditis, and multiple sclerosis.

The complexities of autoimmune diseases lie in the heterogeneity of factors contributing to disease progression and the challenge of pinpointing specific triggers for each individual. Compounding the challenge is the common co-occurrence of multiple autoimmune diseases and other chronic diseases, creating a systemic impact on various organs and tissues. Patients grappling with autoimmune conditions often endure a general sense of unwellness that significantly affects their quality of life. Addressing these complexities requires a comprehensive and collaborative approach between healthcare providers, aiming for symptom management and identifying and mitigating underlying factors contributing to immune system dysregulation.

Standard treatment approaches often involve anti-inflammatory, immunosuppressive, and immunomodulatory medications to mitigate the inflammatory response, but these may have undesirable side effects. Functional medicine, which emphasizes an individualized and holistic approach, is gaining traction in managing autoimmune diseases. Addressing underlying factors such as gut health, nutrition, and stress can be integral in modulating the immune response and managing symptoms. (7

Functional Medicine Lab Testing for Autoimmune Conditions 

Functional medicine lab testing is pivotal in the comprehensive diagnosis and monitoring of autoimmune conditions, offering a more nuanced and personalized approach than traditional diagnostic methods. These specialized tests delve beyond conventional parameters, providing valuable insights into the underlying factors contributing to immune dysregulation.

In the diagnosis phase, functional medicine lab testing can identify specific biomarkers, antibodies, and inflammatory markers associated with various autoimmune diseases. A general screening panel for autoimmune disease will likely include tests like a CBC, ANA Screen + 11 ANA Components, CRP, and ESR (all available from Access Med Labs). Genetic testing may also be employed to assess the individual's susceptibility to autoimmune diseases, further informing the treatment strategy. A typical example is ordering HLA DQ2 and DQ8, genes associated with an increased risk of celiac disease. These genetic markers can be measured on Cell Science Systems' Celiac, IBS, and Crohn's Assay (CICA).

Moreover, functional medicine lab tests facilitate ongoing monitoring of autoimmune conditions. By tracking specific markers of inflammation, immune response, and organ function, healthcare practitioners can assess the progression of the disease and the effectiveness of interventions. This dynamic monitoring allows for timely adjustments to the treatment plan, optimizing outcomes and tailoring interventions to the individual's evolving health status. In addition to serial monitoring of inflammatory markers CRP and ESR, functional medical providers will achieve this by routinely assessing liver and kidney function with a Comprehensive Metabolic Panel by Access Med Labs. In addition to a CBC, functional medicine providers might also recommend ordering the Lymphocyte MAP by Cyrex Laboratories. This immunophenotyping panel provides a broader picture of immune function and status. 

Functional medicine testing extends beyond the conventional scope by exploring factors such as gut health, nutritional imbalances, and environmental toxin exposure. These elements are integral components in the complex web of autoimmune diseases, and their assessment through specialized lab tests enables a more comprehensive understanding of the patient's health landscape. Examples of specialty labs commonly ordered to investigate the intricacy of autoimmune disease in the functional medicine field include: 

  • GI360 by Doctor's Data: This test provides a comprehensive analysis of the gut microbiome's abundance and diversity, screening for pathogenic infections and testing markers of digestion, absorption, and inflammation.
  • Array 12 by Cyrex Laboratories: This is a pathogen-associated immune reactivity screen that examines an individual's immune response to specific pathogens that can increase susceptibility to autoimmune reactions.
  • P88 Dietary Antigen Test IgG/C3d by Precision Point: This test measures IgG antibodies and complement C3d reactions to screen for food sensitivities and associated inflammation. 
  • RTL Tox Complete by RealTime Laboratories: This test bundles the mycotoxin, organic acids, and environmental pollutant panels to assess exposure to various environmental pollutants and mycotoxins and define a patient's toxin burden.


Principles of the AIP Diet

The Autoimmune Protocol (AIP) diet is a therapeutic approach to alleviate autoimmune disease symptoms. Research suggests that damage to the gut barrier leads to increased intestinal permeability and can trigger the development of autoimmune diseases. The core principles of the AIP diet revolve around eliminating inflammatory foods while emphasizing nutrient-dense and anti-inflammatory dietary choices to heal the gut, reduce systemic inflammation, and manage autoimmune symptoms. Through nutritional modifications, the AIP diet serves to reduce inflammation, heal the gut, promote a healthy gut microbiome, and identify dietary triggers of autoimmune disease. (44

AIP Diet Phases

The AIP diet is a modification of the Paleolithic (Paleo) diet, which is rooted in the principles of ancestral eating and advocates for consuming whole, unprocessed foods such as lean meats, fish, fruits, vegetables, nuts, and seeds while excluding grains, legumes, dairy, and processed foods. Like most elimination diets, the AIP diet consists of three phases, described in detail below:


The AIP diet's first phase entails completely eliminating inflammatory foods, including eggs, grains, legumes, nightshade vegetables, nuts, seeds, dairy, added sweeteners, and processed foods. A comprehensive list of foods to avoid is included further down in this article. During this phase, the patient should monitor changes to their symptoms; symptom improvements confirm their symptoms are related to a dietary trigger. While there is no strict guideline on how long this phase should be followed before continuing to the next, most functional medicine providers recommend following an elimination diet for at least four weeks. A plateau in symptom improvement signals it is time to move on to the next phase. (44


The next step is food reintroduction, in which foods are introduced back into the diet one at a time. Each food challenge should be performed over three days (e.g., eat wheat 1-3 times daily for three days). Any foods that provoke unwanted symptoms during this timeframe are removed again. Symptoms should fully resolve before initiating a new food reintroduction challenge. Foods that don't elicit unwanted symptoms can be safely reincorporated into the regular diet. 


The maintenance phase is a long-term customized dietary plan the patient continues to follow using the insights gained during food introductions. The ultimate goal of the AIP diet is to create a sustainable and nutritionally diverse diet that limits individualized food triggers to avoid exacerbating undesirable autoimmune symptoms.

What to Eat on the AIP Diet

The AIP guidelines delineate specific foods to eat and avoid during the elimination phase. (1, 8, 19, 44

Foods to Eat

  • Grass-fed or wild-caught animal proteins: meat, fish, poultry, organ meats, bone broth
  • Fruits: berries, apples, melon, citrus
  • Non-nightshade vegetables: greens, crucifers, cucumbers, zucchini, sweet potatoes, Jerusalem artichoke, parsnips
  • Non-dairy fermented foods: sauerkraut, kimchi, kombucha, pickles
  • Fats and oils: avocado, coconut, olive
  • Herbs and spices: cinnamon, turmeric, thyme, oregano, basil, rosemary 
  • Green tea
  • Maple syrup and honey (in moderation)

Foods to Avoid

  • Grains
  • Legumes: beans, peas, and lentils
  • Nightshade vegetables: tomatoes, potatoes, peppers, eggplant, tomatillos, paprika, cayenne
  • Dairy products: butter, ghee, milk, kefir, cream, cheese
  • Eggs
  • Nuts and seeds
  • Nut and seed oils: canola, walnut, almond, flax, sesame, safflower, sunflower
  • Seed-derived spices: fennel, cumin, dill, anise, mustard, coriander, nutmeg
  • Refined sugars, artificial sweeteners, and food additives (colors, flavors, preservatives)
  • Coffee 
  • Alcohol

Scientific Basis for the AIP Diet

The scientific rationale behind the AIP diet lies in its targeted approach to mitigate inflammation, modulate the immune system, and address underlying factors contributing to autoimmune diseases through dietary modifications. While there is a growing body of anecdotal evidence and clinical observations supporting the benefits of the AIP diet, it is essential to note that large-scale, randomized controlled trials explicitly investigating the AIP diet's efficacy are limited. 

However, several studies have explored the impact of individual components of the AIP diet on autoimmune conditions. For example, research has demonstrated that certain dietary modifications, such as gluten elimination, can positively influence markers of inflammation and autoimmune activity in conditions like celiac disease and Hashimoto's thyroiditis

Let's discuss some of the findings pertaining specifically to the AIP diet in treating autoimmune diseases: 

AIP Diet for Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) refers to a group of chronic inflammatory conditions of the digestive tract, including Crohn's disease and ulcerative colitis, characterized by inflammation and damage to the gastrointestinal lining, leading to symptoms such as abdominal pain, diarrhea, and weight loss.

A 2017 study investigated the impact of the AIP diet on individuals with IBD. After an 11-week AIP elimination diet, significant improvements were noted in IBD symptom scores, fecal calprotectin levels, and endoscopic inflammation. Based on these results, researchers concluded that the AIP diet improved clinical parameters, ameliorated symptoms, and enhanced overall well-being in individuals with IBD.

A 2019 study also examined the impact of the AIP diet on patients with IBD, with similar results. While the study had limitations, such as a small sample size and lack of a control group, patients following an 11-week AIP elimination diet reported improved quality of life as early as three weeks. These results suggest that the AIP diet could have a positive effect on clinical outcomes and quality of life in individuals with IBD.

AIP Diet for Hashimoto's Thyroiditis

Hashimoto's thyroiditis is an autoimmune form of hypothyroidism, accounting for 90% of adult hypothyroidism, that occurs when autoantibodies attack and damage the thyroid gland. According to a 2022 meta-analysis, the global prevalence of Hashimoto's in adults is 7.5%.

A small 2019 study followed 16 women with Hashimoto's thyroiditis adhering to the AIP diet for ten weeks. By the end of the study, inflammation (as measured by hs-CRP) and symptom burden scores decreased by 29% and 68%, respectively. These findings suggest that the AIP has anti-inflammatory and immunomodulatory properties beneficial to patients with autoimmune thyroid disease. 

Implementing the AIP Diet

Successful implementation requires careful planning and commitment for beginners embarking on an AIP diet. Start by thoroughly educating yourself on AIP principles and understanding the foods to include and exclude. Find recipes to form the basis of a simple meal plan, and once you feel comfortable with the principles of the diet, research new AIP recipes to expand your menu options. Before initiating the AIP elimination, stock your pantry with ingredients you will need and remove non-AIP foods for success. Plan meals in advance, focusing on a variety of nutrient-dense options to ensure a balanced diet. When navigating social situations while adhering to the AIP diet, communicate your dietary restrictions with friends and family beforehand and ask for understanding and support. Bringing AIP-friendly dishes to gatherings can help you stay compliant while still enjoying shared meals. It may be helpful to recruit help from a nutritionist or dietician, especially in the beginning stages as you learn to navigate the complexities of AIP.

Challenges and Considerations

One significant challenge of the AIP diet is the restrictive nature of the elimination phase, which involves the extensive removal of various food groups. This strict restriction can make meal planning and dining out challenging, potentially affecting social interactions and overall adherence. Additionally, the elimination of certain food groups may lead to concerns about nutritional adequacy over the long term. Prolonged adherence to the AIP diet without careful planning and monitoring could increase the risk of nutrient deficiencies. To address this challenge, individuals following the AIP diet should work closely with healthcare professionals to ensure a well-balanced and nutritionally sufficient dietary plan, considering potential supplementation if needed and periodically reassessing nutrient levels to mitigate the risk of deficiencies. 

It is common for patients who experience a reduction in symptoms during the elimination phase to be hesitant to move on to food reintroductions for fear of bringing symptoms back. It's important to remember that strict long-term eliminations increase the risk of developing nutrient deficiencies, which can exacerbate chronic diseases. This is why food reintroductions should not be skipped and initiated as soon as possible. 

It may also be worth considering starting with a more moderate elimination diet before embarking on the AIP journey. Simpler, less restrictive elimination diets can include the Paleo, low-FODMAP, and gluten-free diets.

Role of Healthcare Providers in Supporting the AIP Diet

The role of healthcare providers in supporting individuals adopting the AIP diet is paramount to ensuring a safe and effective dietary intervention. Healthcare professionals, including registered dietitians, functional nutritionists, and functional medicine practitioners, play a crucial role in guiding patients through the intricacies of the AIP diet. They can provide comprehensive assessments, including evaluating individual health profiles, identifying potential nutrient deficiencies, and monitoring overall nutritional adequacy to prevent any adverse effects of prolonged dietary restrictions.

Moreover, healthcare providers serve as valuable resources in educating individuals about the AIP diet's scientific rationale, benefits, and limitations. They can help set realistic expectations, address concerns, and provide practical strategies for navigating challenges associated with the elimination phase to improve compliance. Collaborating with healthcare professionals ensures that the AIP diet is seamlessly integrated into a broader healthcare plan that aligns with individual health goals.


The Autoimmune Protocol Diet: Key Takeaways

The Autoimmune Protocol (AIP) diet holds promise as a therapeutic tool in managing autoimmune conditions and enhancing overall quality of life. Preliminary research indicates this diet's promising potential to reduce inflammation, address underlying dietary triggers, promote gut health, and improve the quality of life for people with autoimmune disease. Professional guidance from healthcare providers is indispensable to patients navigating the complexities of the AIP diet. Patient commitment and collaboration between individuals and their doctors are key to optimizing outcomes. By acknowledging the limitations and challenges, tailoring the AIP approach to individual needs, and fostering a supportive healthcare environment, individuals can embark on a journey towards improved well-being, managing autoimmune conditions effectively with dietary-based approaches.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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