What is the 6 week autoimmune diet? Your Guide to the AIP Elimination Phase

October 20, 2025 •

3 min read

According to a 2017 study on inflammatory bowel disease (IBD), 73% of participants achieved clinical remission in just 6 weeks on the Autoimmune Protocol (AIP) diet. So, what is the 6 week autoimmune diet? It refers to the initial elimination phase of the AIP, a nutrient-dense approach designed to reduce inflammation, heal the gut, and identify individual food triggers associated with autoimmune conditions.

Quick Summary

The 6-week autoimmune diet is the first phase of the Autoimmune Protocol (AIP), a dietary plan that eliminates potentially inflammatory foods. It focuses on nutrient-dense foods to reduce symptoms, heal the gut, and identify trigger foods through a systematic reintroduction process.

Key Points

Focused on Reducing Inflammation: The 6-week AIP diet is the initial elimination phase designed to calm the immune system and reduce inflammatory responses in the body.
Systematic Food Identification: The protocol helps you systematically identify specific food triggers by temporarily removing and then carefully reintroducing food groups.
Emphasis on Nutrient-Dense Foods: The diet promotes a focus on highly nourishing foods like vegetables, lean protein, and healthy fats to support healing.
Involves Multiple Phases: This is not a permanent diet; it consists of an elimination phase, a reintroduction phase, and a long-term maintenance phase.
Individualized Healing: The final outcome is a personalized diet plan tailored to your body's specific tolerances and needs.
Best Done with Guidance: Due to its restrictive nature, it is highly recommended to work with a healthcare provider or dietitian to ensure nutritional adequacy.

The 6-week autoimmune diet is the initial elimination phase of the Autoimmune Protocol (AIP) diet. This diet is a more restricted version of the paleo diet, created to help individuals with autoimmune disorders manage symptoms by addressing potential food-related inflammation. The goal is to reduce flare-ups by removing common irritants and focusing on nutrient-rich foods to calm the immune system and heal the gut lining.

Why a 6-Week Elimination Phase?

Autoimmune diseases involve the immune system attacking healthy body cells. It is thought that increased gut permeability, or 'leaky gut', might contribute to this by letting undigested food particles and toxins into the bloodstream, triggering an immune response. The 6-week elimination phase allows the gut time to heal and inflammation to decrease, providing a clearer understanding of how the body reacts to certain foods. While this phase can last longer, 6 weeks is often a starting point to see significant improvements.

The Three Phases of the Autoimmune Protocol (AIP)

1. Elimination Phase (The 6-Week Diet)

This phase is the most restrictive, removing foods thought to cause gut inflammation and overactive immune responses. This includes grains, legumes, dairy, eggs, nuts, seeds, and nightshades. The diet consists of nutrient-dense foods such as wild-caught fish, grass-fed meats, a variety of vegetables (excluding nightshades), fermented foods, and healthy fats. Lifestyle factors like stress management and adequate sleep are also important for healing.

2. Reintroduction Phase

Once symptoms improve, foods are slowly and systematically added back into the diet. This helps identify specific food triggers. For example, egg yolks might be reintroduced before egg whites, or ghee before other dairy. If a food causes a negative reaction, it's removed again. This phase is a careful process of testing and observation, with a 5-7 day gap between reintroducing different foods.

3. Maintenance Phase

After successful reintroductions, a personalized, long-term diet is created that includes well-tolerated foods while minimizing inflammatory ones. The aim is to have the widest possible diet without triggering autoimmune symptoms.

The 6-Week AIP Elimination Phase: What to Eat and Avoid

During the initial 6-week period, the focus is on consuming nutrient-dense, anti-inflammatory foods like meats, fish, vegetables (excluding nightshades), fruits, healthy fats, and fermented foods. Bone broth and fresh herbs are also included. Conversely, foods like grains, legumes, nightshade vegetables, dairy, eggs, nuts, seeds, refined sugars, processed foods, alcohol, and coffee are strictly avoided to allow the body to recover. For a more detailed list of foods to include and avoid during the elimination phase, see {Link: The Pickled Beet https://thepickledbeet.com/special-dietary-needs/aip-diet/}.

AIP vs. Other Elimination Diets: A Comparison


Feature	6-Week AIP Elimination Phase	Paleo Diet	Standard Anti-Inflammatory Diet
Primary Goal	To heal gut and reverse inflammation related to autoimmune disease by identifying personal triggers.	To mimic the diet of Paleolithic ancestors for general health.	To reduce overall systemic inflammation for better health.
Strictness	Very strict; eliminates all grains, legumes, dairy, eggs, nightshades, nuts, and seeds.	Moderately strict; eliminates grains, legumes, dairy, and refined sugar.	Moderately flexible; focuses on increasing anti-inflammatory foods while reducing pro-inflammatory ones.
Key Exclusion	Eggs, nightshades, nuts, and seeds are removed initially.	Eggs, nuts, and seeds are typically included.	Some versions may allow limited amounts of grains, dairy, or nightshades.
Structure	Defined elimination, reintroduction, and maintenance phases.	No formal reintroduction protocol.	Generally ongoing with less formal phases.
Personalization	Highly personalized based on reintroduction results.	Not inherently personalized; individual tolerance testing is not a core principle.	Can be personalized but lacks the systematic reintroduction structure.

Conclusion

The 6 week autoimmune diet, as the initial elimination phase of the Autoimmune Protocol (AIP), is a challenging yet potentially effective approach for managing autoimmune conditions. It provides a structured way to identify personal food triggers and reduce systemic inflammation. Studies, such as one on IBD, have shown positive outcomes like symptom reduction. While initially restrictive, the long-term benefits of a personalized eating plan can be significant. It is important to follow this diet under the guidance of a healthcare professional or dietitian to ensure nutritional needs are met throughout all phases.

For more detailed research on the AIP diet's effectiveness for inflammatory bowel disease, see this study.

Frequently Asked Questions

The main goal is to reduce inflammation and heal the gut by removing potentially inflammatory foods for a period of 4-6 weeks. It serves to identify which foods may be triggering or worsening autoimmune symptoms.

Yes, the '6 week autoimmune diet' typically refers to the initial elimination phase of the Autoimmune Protocol (AIP). The AIP is a multi-phase dietary approach that includes elimination, reintroduction, and maintenance stages.

No, eggs are eliminated during the initial 6-week phase of the AIP diet. They are a common food allergen and a potential source of inflammation for some individuals with autoimmune conditions.

After the 6-week elimination phase, if symptoms have improved, you begin the reintroduction phase. You'll reintroduce eliminated foods one by one to see which ones your body tolerates and which cause a return of symptoms.

While promising, research on the AIP diet is still limited to a few conditions like IBD and Hashimoto's disease. The diet aims to manage symptoms and reduce inflammation, but individual results vary, and it is not a universal cure.

If there is no improvement, it may indicate that food triggers are not the primary cause of your symptoms, or that other lifestyle factors (like sleep or stress) need addressing. A dietitian can help evaluate other strategies.

Because the AIP elimination phase is restrictive, it is not recommended to follow it without professional guidance from a doctor or dietitian. They can help ensure you meet your nutritional needs and manage the process safely.