What are the stages of the autoimmune protocol? An in-depth guide

October 9, 2025 •

3 min read

Autoimmune diseases affect an estimated 23.5 million Americans and are a leading cause of morbidity. For many, diet plays a significant role in managing symptoms, and the Autoimmune Protocol (AIP) is designed to help identify and address food triggers through a structured, multi-stage approach.

Quick Summary

The autoimmune protocol is a three-phase dietary strategy involving the elimination of inflammatory foods, a methodical reintroduction of foods, and a personalized long-term maintenance plan.

Key Points

Three-Phase Process: AIP is composed of three distinct stages: elimination, reintroduction, and maintenance.
Elimination Phase: This first stage involves strictly removing common inflammatory foods for at least 30 days to allow the body to heal.
Reintroduction Phase: This stage requires systematically adding foods back one at a time to identify which ones trigger symptoms.
Maintenance Phase: The final stage is a personalized, long-term dietary plan based on what was learned during reintroduction.
Gut Health Focus: The core principle of AIP is to heal and restore gut health, which is thought to be central to immune function.
Personalization is Key: No two AIP journeys are identical; the goal is to discover what works for your unique body.
Professional Guidance: Working with a healthcare provider is recommended to navigate the diet and ensure all nutritional needs are met.

Understanding the Autoimmune Protocol (AIP)

The Autoimmune Protocol (AIP) is an extension of the Paleo diet designed to reduce inflammation and symptoms in individuals with autoimmune conditions. It focuses on gut healing, considered crucial for immune function. AIP helps individuals identify personal food triggers and build a sustainable, customized diet. The AIP journey is structured into three key stages: Elimination, Reintroduction, and Maintenance.

Stage 1: The Elimination Phase

This initial phase involves removing foods and substances that commonly trigger inflammation, intestinal damage, or gut microbiota imbalances. It typically lasts at least 30 days, or longer depending on symptom improvement. This allows the body to recover from potential inflammatory triggers. During this phase, you remove grains, legumes, nightshade vegetables, dairy, eggs, nuts, seeds, processed foods, additives, alcohol, and coffee. The diet focuses on nutrient-dense whole foods like lean protein, vegetables, fruits, healthy fats, fermented foods, and bone broth.

Stage 2: The Reintroduction Phase

Once symptoms improve, the reintroduction phase begins. This methodical process of reintroducing one food at a time helps identify individual triggers. Reintroductions are often done in four stages, moving from foods least likely to cause a reaction to those most likely. The method involves testing a small amount, observing for reactions, and then if tolerated, reintroducing a normal portion followed by an observation period before testing the next food.

Stage 3: The Maintenance Phase

After reintroduction, the maintenance phase involves a lifelong, personalized eating plan based on identified food triggers. This phase aims to maintain a diverse diet while avoiding foods that cause flare-ups. It's about empowering individuals to manage their health long-term. Food tolerances can change, and previously failed foods can sometimes be re-challenged later. Professional guidance is recommended during maintenance to ensure nutritional needs are met.

AIP Stages: A Comparison


Feature	Elimination Phase	Reintroduction Phase	Maintenance Phase
Goal	Reduce inflammation and heal the gut by removing potential triggers.	Systematically identify individual food triggers by testing one food at a time.	Maintain a personalized diet that avoids triggers and supports long-term health.
Duration	30-90 days, or until significant symptom improvement is noted.	Varies greatly; can take several months to a year or more.	Lifelong, with potential for periodic adjustments and re-testing.
Restriction Level	Very high; removes all common inflammatory food groups.	Moderate, with tested and tolerated foods being reincorporated.	Low, based on personal tolerance and avoiding only specific triggers.
Allowed Foods	Whole foods like meats, fish, vegetables (non-nightshade), fruits, healthy fats, and fermented foods.	Includes all foods from the elimination phase plus any new foods that have been successfully re-challenged.	A personalized list of tolerated foods from the reintroduction phase, aiming for maximum diversity.
Key Action	Strict removal of problematic foods.	Careful, one-by-one re-testing and observation.	Sustainable lifestyle based on individual food sensitivities.

Conclusion

The autoimmune protocol is a structured dietary approach to manage autoimmune symptoms. By progressing through the elimination, reintroduction, and maintenance phases, individuals can identify triggers and create a personalized diet. The goal is a sustainable lifestyle minimizing inflammation and optimizing health. Consulting a healthcare professional is vital for guidance and ensuring proper nutrition.

For more information on the protocol, consider referencing the {Link: National Institutes of Health (NIH) https://pmc.ncbi.nlm.nih.gov/articles/PMC11755016/} for supporting research.

Frequently Asked Questions

The elimination phase typically lasts between 30 and 90 days, or until symptoms improve significantly. The reintroduction phase can last several months to a year, as it involves carefully testing one food at a time. The maintenance phase is a lifelong commitment based on your individual food tolerances.

The elimination phase removes grains, legumes, dairy, eggs, nuts, seeds, nightshade vegetables, refined sugars, processed oils, alcohol, and coffee.

To reintroduce a food, eat a small amount and observe for reactions over 15 minutes to a few hours. If no symptoms occur, eat a normal portion and then avoid that food for 5-7 days while monitoring for any delayed reactions.

It is not recommended to skip the reintroduction phase. This stage is crucial for identifying your personal trigger foods and expanding your diet as much as possible for long-term nutritional variety and flexibility.

If a food causes a return of symptoms during the reintroduction period, you should remove it from your diet. You can retry reintroducing it later, after a period of further healing, but you must move on to testing other foods in the meantime.

No, AIP is not meant to be followed indefinitely. After the elimination and reintroduction phases, the goal is to create a personalized, sustainable maintenance diet that includes all tolerated foods while avoiding specific triggers.

The main benefits include a reduction in inflammation, improved gut health, identifying personal food triggers, and potential relief from symptoms associated with various autoimmune diseases.

It is highly recommended to consult with a healthcare provider or a registered dietitian before and during the AIP process. They can provide guidance, monitor for nutrient deficiencies, and help you navigate the stages safely and effectively.