How To Do an Elimination Diet or Autoimmune Paleo Protocol

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How To Do an Elimination Diet (or Autoimmune Paleo Protocol)


An Elimination Diet is exactly what it sounds like - a diet that eliminates certain foods that could potentially be causing a problem in your body - the most common offenders being gluten, dairy, eggs, corn, and soy, and sometimes nuts or even nightshade vegetables like tomatoes and peppers. These foods are eliminated from the diet for a period of time with hopes that your body “resets” and becomes less reactive. The foods are then re-introduced gradually as you observe for any negative responses, like headaches, brain fog, digestive complaints, and more (discussed below). The foods you choose to eliminate are what differentiate an Elimination Diet from an Autoimmune Paleo Protocol (AIP). An Elimination Diet is more basic - you cut out the MOST inflammatory foods. The Autoimmune Paleo Protocol is more advanced - you cut out ALL of the potentially inflammatory foods, because these foods could be pouring gas on your autoimmune “fire”.


Food sensitivities are a frequently overlooked cause of chronic health issues. Certain foods can trigger immune reactions in certain people. You may have known someone with a food allergy, like peanuts for example, which can be life-threatening. Food sensitivities are similar, but different. Allergies are a different immune response than a “sensitivity” reaction. Allergies are often an immediate response (hives, throat swelling shut), whereas a food sensitivity could take days to show up (in the podcast I discuss the difference between an IgE allergic response and an IgA or IgG-mediated delayed response, which are more typically the target of the elimination diet). This means that your pizza and beer on Friday night could be the cause of your brain fog on Monday morning!  

This inflammatory response from your immune system can create symptoms such as digestive problems, headaches, brain fog, skin issues like acne, eczema, psoriasis, joint pain, mood swings, depression, anxiety, and fuel autoimmune conditions like Hashimoto’s thyroiditis, multiple sclerosis, lupus, rheumatoid arthritis, Crohn’s disease, and many more (hence the name of the diet - Autoimmune Paleo Protocol). There are a number of factors that contribute to the cause - genetic predispositions, how often you eat a food (when you eat a food often it’s more likely to be a trigger food), toxic burden throughout life, your microbiome and gut health, immune system balance - but when a food is triggering an immune response it can be like pouring a little bit of gas on your inflammatory fire.


*This is an overview. Please listen to the podcast for more information, and download the attached PDFs for more detailed instruction on exactly what you CAN and CANNOT eat.

A typical Elimination Diet eliminates the most foods that most commonly elicit an immune reaction, including:

  • Gluten-containing grains

  • Dairy

  • Eggs

  • Corn

  • Peanuts

  • Soy

  • Pork or Beef (sometimes)

  • Sugar(s)

  • Processed Foods

  • Coffee

  • Alcohol

The Autoimmune Paleo Protocol takes it a step further. A “Paleo” diet is already free of processed foods and sugars, and it’s already grain-free, dairy-free, and legume-free, and limits many nightshades like potatoes. The Autoimmune Paleo Protocol ALSO eliminates:

  • ALL Grains - wheat, rye, barley, corn, rice - that’s bread, crackers, wraps, everything

  • ALL Nuts

  • ALL Seeds

  • Legumes (ALL beans and peas)

  • Nightshades (peppers - cayenne, bell, et, goji berries, eggplant, tomatoes, potatoes (sweet potatoes are okay), paprika)

The goal is eliminating these foods from your diet for a period of time and allowing your body and immune system to “reset”, and then you gradually begin to re-introduce the foods. I typically have clients remove foods for THREE WEEKS, and then begin re-introducing foods one at a time every THREE DAYS.

Food Re-Introduction

The goal with re-introducing your “eliminated” foods is to go slowly so you can evaluate whether or not you are experiencing any negative response. If you break your Elimination Diet with pizza and you feel horrible the next day you have to ask yourself, “Was it the gluten in the dough, the dairy cheese, the nightshade sauce, the processed pepperoni, or any of the other potential triggers?” It’s impossible to know, so it’s important to re-introduce foods one-at-a-time and slowly, because sensitivities can take several days to show up. I recommend a three-day window - re-introduce a food for three days, wait to see if you notice any negative response, if you DO - stop the food immediately and continue to challenge the other foods, if you DON’T notice any response in three days then re-introduce another food.

How Do I Know What Plan To Follow?

Any version of an Elimination Diet could potentially be successful. The Whole30 is a tremendously successful Elimination Diet eating plan that cuts out processed foods, sugars, grains, dairy, legumes, alcohol I personally have more experience with the stricter Autoimmune Paleo Protocol because we see a lot of people in our clinic that have autoimmune conditions and they have typically already cleaned their diet up considerably or tried different diet plans (they have often already gone gluten-free, dairy-free, done a Whole30, etc). I mention in the podcast that we recently did a recipe night at our clinic where people brought their homemade AIP-approved meals and we had a big, healthy potluck. I typically recommend EVERYONE eliminate certain foods - sugar and processed foods, gluten and other grains, sometimes dairy, and then I often make custom recommendations based on a client’s history and symptoms.

If you are someone listening to this podcast and you are curious, download the attached PDFs from the Institute for Functional Medicine and try the Elimination Diet. If you are someone who KNOWS that you have an autoimmune disease, or you think your health symptoms are related to certain foods - try the AIP protocol.

Here are some great AIP resources:

Autoimmune Paleo Cookbook - Mickey Trescott

The Essential AIP Cookbook - Louise Hendon

The Paleo Approach - Reverse Autoimmune Disease and Heal Your Life - Sarah Ballantyne PhD

The Paleo Approach Cookbook

Other Potential Triggers:

Often people will notice that a particular “group” of foods cause reactions. In this podcast I briefly discuss several of these food groups you can look out for, including:

  • Histamines

  • Oxalates

  • Salicylates

  • Nightshades

  • Lectins


These particular groups of foods have been found to be problematic for many people. In the podcast I discuss a newer book called The Plant Paradox by Dr. Stephen Gundry where he discusses the dangers of lectins, which are found in many plants including legumes, nuts, and many vegetables. These food categories are worth looking into further if you aren’t getting the results you had hoped for with the Elimination Diet.


This involves A LOT OF TRIAL AND ERROR! It’s not easy to discover your triggers. It takes time. Sometimes you will find one and think “This is my answer I’ve been looking for!” and although it may be an important piece of the puzzle, down the road you could discover other triggers, new symptoms, etc. Don’t be disappointed, just keep moving forward. Your health is a never-ending journey!

When it comes to inflammation, anything that pours even a little bit of gas on the fire can flare up your symptoms, so this is a long-term battle - but the great news is that it GETS EASIER. You learn about yourself and your body. You learn new shopping habits, you learn how to cook with different ingredients, and your immune system becomes more balanced and less responsive.

If you are working with a practitioner he or she may be providing additional supplement support to balance the immune system, support digestion, or help heal a leaky gut, which can help support the process. If you are not, this can make a huge difference!

This isn’t a magic bullet cure. This is PART of your personal inflammation puzzle, and often a big part. If there are other sources of inflammation - toxins, stress, poor gut health, sedentary lifestyle, poor blood sugar control, hormone imbalance - an Elimination Diet is an important foundational step but it’s NOT a magic bullet, but rather a piece of the health puzzle.

The Elimination Diet Comprehensive Guide