Can You Eat Eggs on Autoimmune Paleo? An AIP Reintroduction Guide

January 3, 2026 •

5 min read

According to the Autoimmune Protocol (AIP) framework, eggs are excluded from the initial elimination phase to reduce inflammation and support gut healing. While considered healthy on a standard Paleo diet, their potential allergenic proteins make them a suspect food for those with autoimmune conditions during the elimination phase.

Quick Summary

The AIP diet removes eggs due to potential allergenic proteins in the whites and inflammatory compounds in the yolks. They can be systematically reintroduced to test individual tolerance.

Key Points

Initial Elimination: During the first phase of the AIP diet, eggs must be completely eliminated to aid in gut healing and reduce inflammation.
Why Eggs are Excluded: Egg whites contain proteins like lysozyme and avidin, which can be allergenic and increase intestinal permeability ('leaky gut'). Egg yolks contain arachidonic acid, an omega-6 fatty acid that can be inflammatory in excess.
Reintroduction Process: Eggs can be reintroduced after a period of symptom relief (typically 30-90 days), following a careful, one-food-at-a-time protocol.
Start with Yolks: Egg yolks are generally better tolerated than whites. It is recommended to reintroduce yolks first and wait for a period of observation before testing whole eggs.
Observe for Reactions: Track a food and symptom journal during reintroduction, watching for digestive issues, fatigue, or skin problems. If symptoms appear, remove eggs again.
Personalized Results: The outcome is individual. Some people tolerate eggs well after reintroduction, some can only tolerate yolks, while others may need to avoid them long-term.

The AIP Elimination Phase: Why Eggs Are Excluded

The Autoimmune Paleo (AIP) diet is a specialized, stricter version of the standard Paleo diet designed to manage and reduce symptoms associated with autoimmune diseases. The core principle involves a temporary elimination phase followed by a systematic reintroduction of foods to identify individual triggers. Unlike traditional Paleo, which embraces eggs, the AIP protocol mandates their temporary removal for a specific set of reasons related to gut health and immune response.

Potential Issues with Egg Whites

The primary reason for eliminating eggs during AIP is centered on the egg whites, which are a common allergen. Egg whites contain proteins like lysozyme and avidin that can be difficult for a compromised gut to process. For individuals with autoimmune conditions and a potentially permeable intestinal lining, or 'leaky gut', these undigested proteins can pass into the bloodstream. The body may then perceive these proteins as foreign invaders, triggering an immune response and perpetuating the inflammatory cycle. This reaction is a central concern for individuals trying to calm an overactive immune system through diet.

Concerns with Egg Yolks

While generally better tolerated than the whites, egg yolks are also eliminated during the initial phase. Egg yolks contain arachidonic acid, an omega-6 fatty acid that, in excess, can promote inflammation. While omega-6 fatty acids are essential, the goal of the AIP elimination phase is to remove all potential inflammatory burdens to give the body a clean slate to heal. During this period, the focus shifts to sourcing omega-3s from other AIP-compliant sources like wild-caught fish, balancing the body's fatty acid profile.

When and How to Reintroduce Eggs on AIP

The reintroduction of eggs is a key part of the AIP process, not a permanent exclusion. The timing depends on your individual healing progress. Most practitioners recommend waiting until you have experienced a significant reduction or total remission of your autoimmune symptoms, which can take anywhere from 30 to 90 days. The process is highly personalized and requires careful, methodical steps to accurately identify any adverse reactions.

Staged Egg Reintroduction

The most common approach is to reintroduce eggs in stages, starting with the least allergenic part—the yolk. This minimizes the risk of a reaction while still testing for tolerance. Wait at least five days between each reintroduction to observe for delayed symptoms.

Stage 1: Egg Yolks

On your reintroduction day, eat a very small amount (e.g., half a teaspoon) of a pasture-raised egg yolk. Wait 15 minutes and monitor for immediate symptoms.
If no symptoms appear, eat a slightly larger portion (e.g., one teaspoon) and wait 2-3 hours.
If still no reaction, eat a normal-sized portion and refrain from eating that food again for five days while monitoring for delayed symptoms.
If you tolerate the yolks with no adverse effects, you can incorporate them into your diet regularly and proceed to the next stage.

Stage 2: Egg Whites

Repeat the same careful, gradual testing process using a whole egg (including the white).
Start with a small amount of a whole scrambled or soft-boiled egg and follow the same waiting and observation protocol.
Remember to wait five days between testing the yolks and the whole eggs.

Egg Tolerance: What to Observe

During the reintroduction phase, it is crucial to keep a food and symptom journal to track any potential reactions. Symptoms can vary widely and may not appear immediately, underscoring the need for the five-day observation period. Look for signs such as:

Digestive issues (e.g., bloating, gas, stomach pain)
Skin reactions (e.g., hives, rashes, eczema)
Joint pain or muscle aches
Fatigue or changes in energy levels
Headaches
Mood changes (e.g., anxiety, irritability)

If any of these symptoms appear, stop eating eggs immediately and allow your body to reset. You can try reintroducing them again in the future after a more extended healing period.

AIP vs. Paleo Egg Rules: A Comparison


Feature	Standard Paleo Diet	Autoimmune Protocol (AIP)	Note on Eggs
Eggs	Allowed	Excluded during elimination phase	AIP is stricter, removing potential allergens
Focus	Ancestral eating, whole foods	Healing the gut lining and reducing inflammation	AIP adds a therapeutic layer for autoimmune conditions
Grains	Excluded	Excluded	Both diets remove grains
Legumes	Excluded	Excluded (including green beans and peas)	AIP is more restrictive here, excluding even podded legumes
Nightshades	Allowed	Excluded during elimination phase	Another key difference, as AIP removes potatoes, tomatoes, and peppers
Dairy	Excluded (often)	Excluded	Neither diet allows most dairy
Reintroduction	Not a formal process	A core, systematic phase	AIP's methodical reintroduction is crucial for personalization

AIP-Compliant Egg Replacements

While abstaining from eggs, many people seek AIP-compliant alternatives for cooking and baking. These can effectively replace eggs' binding, leavening, and moisturizing functions.

Mashed Banana: Excellent for adding moisture and binding baked goods.
Applesauce: A fruit-based substitute for moisture, especially in sweet recipes.
Pumpkin Purée: Provides moisture and binding properties, particularly useful in baked treats.
Gelatin Egg: A mixture of gelatin powder and water that can be used as a binder in many recipes.
Arrowroot Powder: Can be mixed with water to form a binding paste.
Vinegar and Baking Soda: Creates a leavening reaction, mimicking the effect of eggs in some recipes.

Conclusion: A Personalized Approach to Eggs and AIP

In short, you cannot eat eggs during the elimination phase of the Autoimmune Paleo diet. This strict, temporary exclusion serves to minimize inflammatory triggers and allow for gut healing. However, the restriction is not meant to be permanent. The systematic reintroduction phase is the most critical step, empowering you to test your individual tolerance to eggs and other eliminated foods. By listening to your body's feedback, you can determine if and how eggs fit into your long-term, personalized AIP-based diet. A methodical approach, starting with yolks and carefully observing symptoms, is the key to successfully navigating this dietary protocol. Remember, the goal is not a lifetime of restriction but a personalized plan for managing your autoimmune health.

For more detailed information on the AIP diet and its phases, you can explore scientific resources like this paper from the National Institutes of Health.

Frequently Asked Questions

Eggs are eliminated during the AIP's initial phase because egg whites contain allergenic proteins (lysozyme and avidin) that can irritate the gut lining, and egg yolks contain an omega-6 fatty acid (arachidonic acid) that can be pro-inflammatory.

Yes. The Paleo diet permits eggs, as it focuses on ancestral eating patterns. The AIP diet is a more restrictive version of Paleo, specifically designed as an elimination protocol for autoimmune diseases, requiring eggs to be removed temporarily.

After achieving significant symptom improvement, reintroduce eggs systematically. Start with egg yolks only in small amounts, observe for five days, and if no reaction, then move on to testing whole eggs. Monitor symptoms closely throughout.

This is a common outcome. Some individuals find that while egg whites trigger symptoms, the yolks are well-tolerated. It's acceptable to reintroduce only egg yolks and continue avoiding egg whites if that is what your body can handle.

The total process can take several weeks, as each stage of reintroduction (yolks, then whites) requires a period of observation, usually around five to seven days, to watch for any delayed reactions.

You can use alternatives like mashed banana, applesauce, pumpkin purée, gelatin eggs (gelatin and water), or arrowroot powder with water to mimic the binding and moisturizing properties of eggs in recipes.

Yes. If an initial reintroduction of eggs causes symptoms, you should return to the elimination phase until symptoms subside. After a period of healing, you can attempt the reintroduction process again.