Getting Started on The Paleo Autoimmune Protocol

Getting Started on The Paleo Autoimmune Protocol

paleo autoimmune protocol

The Paleo Autoimmune Protocol is a version of the Paleo diet that focuses on healing the gut and reducing inflammation in the body to improve symptoms of autoimmunity, digestive disorders, or other health concerns that are related to a compromised gut. In addition to eliminating the foods that are restricted in a general Paleo nutrition template, the Paleo Autoimmune Protocol takes it a step further by temporarily removing certain foods, gut irritants, and environmental factors that are known to have a negative impact on gut health. The foods that are restricted on the Paleo Autoimmune Protocol include:

Eliminate Permanently Eliminate for a Minimum of 30 Days, Then Reintroduce
Grains Eggs
Legumes All Dairy (Including Grassfed Butter)
Processed Dairy Nuts
Refined Sugars Seeds (Including Cocoa and Coffee)
Refined Fats & Oils Seed-based Spices (Dill, Fennel, Sesame Seed, etc.)
All Processed Foods Nightshade Vegetables (Including Tomatoes, Eggplants, Potatoes, Peppers, Tomatillos, Spices Derived from Peppers, etc.)

Other Factors to Consider

Stress reduction and adequate sleep are both key elements to implementing the Paleo Autoimmune Protocol, as well as restricting high intensity and chronic endurance exercise. The body’s overall toxic burden should be minimized by reducing exposure to toxic cleaning products and conventional hygiene and beauty care products. 

Although you should consult with your provider prior to discontinuing any prescribed medications, the use of over-the-counter pain medications, such as NSAIDs (aspirin and ibuprofen) and acetaminophen can interfere with the healing process while following the protocol. 

Many prescription medications, such as hormonal birth control and corticosteroids also affect the gut, which may be something to consider if the Paleo Autoimmune Protocol is not working well for you. Consuming nutrient-dense foods, such as organ meats and bone broth, and monitoring the use of Paleo-friendly sweeteners is also advised.

Is the Paleo Autoimmune Protocol Right for You?

If you are struggling with symptoms of autoimmunity, digestive distress, or other nagging health concerns, you should first consider transitioning to a general Paleo nutrition template, if you have not done so already. Many people discover that the general Paleo diet works well to control their symptoms and improve their quality of life.

If you are still having distressing symptoms despite following a strict Paleo diet, you may then want to consider the Paleo Autoimmune Protocol. You do not need to be officially diagnosed with an autoimmune disease to try the protocol. Some types of autoimmune disease are notoriously difficult to diagnose and waiting for a diagnosis isn’t necessary.  If followed correctly, the Paleo Autoimmune Protocol is a balanced, nutrient-dense diet.

Why the Paleo Autoimmune Protocol Works

The intestinal lining is one of the immune system’s major lines of defense against infections, toxins, and other threats that are introduced into the body through food and drink. Normally, the intestinal epithelial cells sit together closely and are joined by tight junctions that form a barrier to prevent unwanted substances from passing through into the bloodstream. 

The lining of the small intestine can become damaged due to a variety of factors, leading to what is referred to as a leaky gut.  The leaky gut will allow undesirable substances to pass directly from the gut to the bloodstream. The body recognizes these substances as foreign invaders and mounts an immune system attack. Research suggests that a leaky gut can eventually lead to systemic inflammation and autoimmunity. 

The Paleo Autoimmune Protocol focuses on healing the lining of the small intestine to decrease the permeability. The foods and environmental considerations that are restricted on the protocol are those that are known to increase intestinal permeability or cause inflammation in the body. 

By eliminating these factors for a period of time, the lining of the gut is given an opportunity to heal and become less permeable.  Often, it may be possible to reintroduce these foods without having a reaction or a return of symptoms.  Other times, it may be possible to reintroduce some of the foods, but not all of them.

Reintroducing Foods on the Paleo Autoimmune Protocol

If attempting the Paleo Autoimmune Protocol, all of the restrictions should be implemented for a minimum of 30 days, or ideally, until symptoms have improved before attempting a reintroduction. Foods should be reintroduced one at a time, waiting at least 3 days in-between food reintroductions to monitor for any symptoms of sensitivity or reaction to the food. Symptoms that indicate a reaction to food include a return of autoimmune symptoms, gastrointestinal distress, joint pain, headache, fatigue, skin changes, or mood fluctuations. 

While the Paleo Autoimmune Protocol can be challenging to implement, it has been known to drastically improve the quality of life of many people struggling with a variety of health concerns.  Have you tried the Paleo Autoimmune Protocol?  What has your experience been like?



8 Responses

    • Fats are neither inherently good nor bad as they are found in nature–the difference lies in how they are processed. Refined fats and oils are those that have undergone significant processing that involves high heat and/or chemically-based processes. This includes hydrogenated and partially hydrogenated oils, trans fat (a byproduct of hydrogenation), many types of vegetable oils that are not cold pressed or unrefined, canola oil, soy oil, cottonseed oil, and any manmade fats or oils.

      Processed dairy is what you will typically find in a general supermarket. It is dairy that has been altered from the raw state by pasteurization, irradiation, or homogenization. Many contemporary Paleo followers will allow some high quality dairy into their diet in the form of grass-fed, organic butter. The inclusion of raw dairy is generally considered more of a Primal perspective. A lot of people with autoimmune disease that I work with have sensitivities to processed dairy, but if they focus on healing their gut, they may find that they can eventually tolerate some amounts of high quality butter and even some raw dairy once in a while. Raw dairy has all of the enzymes and nutrients intact. The enzymes in the raw dairy allows for easier digestion for some people.

  1. I’m very interested to start this. I have a type of auto immune arthritis that keeps progressing. I just need to get organized. I brought the auto immune cookbook and the whole30 start plan.

  2. I am 3 days in to AIP with MS. I also have been paleo and did a Whole30 before this, but got off track with traveling and other roadblocks… Excited to stick to it for good this time!!

  3. This is not based on a true paleo diet. There is so little nutrition fact here. Please do your due diligence. Dairy, refined or not, has IGF-1 which is associated with increases in the autoimmune diseases these commenter have stated they hope this diet will alleviate.

    • Specific to the Paleo Autoimmune Protocol, I don’t believe that dairy is the best choice for people who are struggling to get their autoimmune disease under control, nor did I ever say that it was. I was simply explaining the difference between processed and raw dairy. Some people do tolerate raw dairy better than processed. Does that mean everyone will be able to tolerate dairy? Definitely not. There are a lot of compelling reasons to avoid it–it is highly allergenic, cross-reacts with gluten, contains IGF-1, etc. On the other hand, there is research that demonstrates dairy can be beneficial and healthful if it is well-tolerated–it is a rich source of fat soluble vitamins, CLA, glutathione, calcium, etc.

      The reasoning for choosing or excluding foods should not be centered around reenacting a “true” Paleo diet. There are a lot of modern foods that weren’t available to our paleolithic ancestors, yet they can still be nutrient-dense and healthy to consume. I firmly believe in a Paleo template, but I also believe that people should choose foods based on how their bodies respond, not simply on a dogmatic perspective of a Paleolithic diet.

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