What is Autoimmune Paleo?

An elimination protocol designed to aid in healing
Autoimmune Paleo

What is the Autoimmune Protocol (AIP)?

The Autoimmune Protocol is a redefined version of the Paleo diet, with a greater focus on nutrient density and even stricter guidelines for which foods are eliminated. Foods can be categorized in two separate groups, nutrient dense and inflammatory. Now, I must say that a specific type of food might cause inflammation in my body while promoting healing for another, like pineapple. I cannot tolerate pineapple in any form but it is still rich in nutrients like Thiamin, Riboflavin, vitamin B-6, Folate, Pantothenic Acid, Magnesium, Manganese & potassium that are wonderful for the average person who can digest it properly. These superfoods are included on the Autoimmune Protocol because they are jam packed with tons of nutrients and are easily tolerate by most people: organ meats, seafood, and most vegetables. Examples of foods that are not digested well include gluten-containing grains including corn, dairy, peanuts, most soy products, refined sugars and refined oils. But there are still a handful of whole foods that fall into the wide world of gray in between nutrient-density and inflammatory.

"The biggest difference between a standard Paleo diet and the Autoimmune Protocol is where we draw the line between “yes” foods and “no” foods in order to get more health-promoting compounds and fewer detrimental compounds in our diet" states Dr. Sarah Ballantyne, author at The Paleo Mom https://www.thepaleomom.com/start-here/the-autoimmune-protocol/

The Autoimmune Protocol is designed to promote gut healing by eliminating foods including nightshades (white potatoes, all peppers, tomatoes and eggplant), eggs, nuts, seeds, alcohol, NSAIDS, emulsifiers & thickeners because these ingredients contain compounds that may stimulate the immune system or cause harm to our gut environment. The goal of the Autoimmune Protocol is to flood the body with as many nutrients as possible while simultaneously avoiding any food that might be contributing to disease or interfering with our chance to heal the gut. It is an elimination diet cutting out wheat, gluten, grains, dairy, soy, legumes, nightshades, eggs, nuts, seeds, refined oils, refined sugars, chocolate and alcohol.

The Protocol

How does the Autoimmune Protocol work?

The Paleo Autoimmune Protocol works by addressing four key areas known to be important contributors to chronic and autoimmune diseases:

  1. Nutrient density. Our bodies require an array of vitamins, minerals, antioxidants, essential fatty acids, and amino acids to function normally and most of us are not getting the necessary daily amounts we need with the Standard American Diet (SAD). Thus, a severe lack of micronutrients and imbalances will lead to the development and progression of any type of chronic disease in the human body. With the Atoimmune Protocol, it allows us to focusing on flooding our bodies with the most nutrient-dense foods available and creates a synergistic surplus of micronutrients to correct both deficiencies and imbalances that have developed over our lifetime, maybe even while we were in our mother's womb. This nutrient-dense protocol assist in supporting regulation of the immune system, hormone systems, detoxification systems, and neurotransmitter production. Basically, we are flooding our body with healthy nutrients, vitamins and minerals to both heal current damage to our tissues and prevent potential health challenges in the future.
  2. Gut health. Have you ever heard of Leaky Gut? Yeah, me neither, until I started suffering from the most random symptoms and an acupuncturist educated me about Leaky Gut. Gut dysbiosis and leaky gut are key facilitators in the development of inflammation and disease in the body. The whole foods listed on the Paleo Autoimmune Protocol support the growth of healthy levels and a healthy variety of gut bacteria (microorganisms).
  3. Hormone regulation. I always thought that hormones were solely related to our sex drive and reproductive system, boy was I in for a surprise! What we eat, when we eat, and how much we eat affect a variety of hormones that interact with the immune system. The Paleo Autoimmune Protocol diet is designed to promote regulation of these hormones alongside responsible lifestyle choices such as regulating stress management, spending time with mother nature, partaking in daily exercise & getting adequate hours of sleep each and every night of our lives.
  4. Immune system regulation. Immune regulation is achieved by restoring a healthy diversity and healthy amounts of gut microorganisms, restoring the barrier function of the gut and regulating the key hormones that in turn regulate the immune system.

Inflammation is a factor in all chronic illnesses and most of us don't even realize how depleted our bodies are of nutrients until we are uncontrollably ill and/or hospitalized. Our bodies give us so many small signs along the way but we are not paying close enough attention to know when or how to change our daily habits. This is one area where the foods we eat can make a huge difference if we just allow it! What this means is that reducing inflammation and giving our immune system the resources it needs, as well as the opportunity to regulate itself can repair years of damage and (hopefully) prevent future damage. This is important because inflammation is strongly influenced by what we eat, how well we sleep, how stressed we are, and how active we are. This concept took me a long time to realize and understand but it is undoubtedly true that humans can respond so positively to changes in diet and lifestyle.

Now, I must say that even though food is medicine, food is not the ultimate cure! I completely changed my diet and lifestyle but I still need pharmaceutical medication from time-to-time as well as supplements and Chinese herbs to keep my body regulated.

I know, I know, it sounds like there is nothing left to eat but please shift your perspective 180 degrees and focus on what you CAN eat:

  • organ meat and offal (aim for 5 times per week, the more the better)
  • fish and shellfish (wild is best) (aim for at least 3 times per week, the more the better)
  • vegetables of all kinds, as much variety as possible and the whole rainbow, aim for 8-14 cups per day
  • herbs and spices (except nut and seed based spices)
  • quality meats (grass-fed, pasture-raised, wild as much as possible)
  • quality fats (pasture-raised/grass-fed animal fats, fatty fish, olive, avocado, coconut, palm oil)
  • fruit (keeping fructose intake between 10g and 20g daily)
  • probiotic/fermented foods (fermented vegetables or fruit, kombucha, water kefir, coconut milk kefir, coconut milk yogurt, supplements).
  • glycine-rich foods (anything with connective tissue, joints or skin, organ meat, and bone broth)
  • Source the best-quality ingredients you can including organic produce.
  • Eat as much variety as possible.

How long is this protocol?

That's the beauty of it, you eliminate these foods for 30-days (minimum) and start reintroducing the items one by one. This provides you the opportunity to really get to know your body and learn what causes inflammation specifically for Y.O.U.! Personally, I was in the elimination phase for 90-days (January 2017-March 2017) until I started reintroducing foods and I am still reintroducing them to this day (December 2017). It takes time, my friends, and I know it's tempting to rush because I did that to myself but then I noticed that I was losing track of which ingredients were causing a reaction and which weren't, then I had to eliminate those items all over again and that pushed me back 1-2 months every time I rushed them. It's just not worth rushing!!!

This elimination diet is not meant to last forever and I know that sometimes it might feel as if you are still suffering, the truth is that your body is HEALING, I promise you. Every additional moment of patience, compassion and love adds to the healing journey and your body is thanking you for it.

Which Foods Are Eliminated?


The eliminated foods in a Paleo diet are ones that contain very little nutrition and are difficult to digest because this may lead to the simulation of inflammation or negatively affect important hormones. This could cause much distress and infertility as well. Generally, a Paleo diet excludes: grains and pseudograins legumes (legumes with edible pods […]

What Foods Are Included?


I asked myself this very same question over and over again when I was first wrapping my brain around this new way of eating and living. Transitioning from a vegetarian ultra-runner who lived off of breakfast burritos, chocolate cake & Buddha Bowls, trust me when I said this transition was more difficult than any Ultra-marathon […]

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