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A Functional Medicine Expert's No. 1 Diet For Autoimmunity + What To Try If It Doesn't Work For You

William Cole, IFMCP, DNM, D.C.
November 24, 2021
William Cole, IFMCP, DNM, D.C.
Functional Medicine Practitioner
By William Cole, IFMCP, DNM, D.C.
Functional Medicine Practitioner
Will Cole, IFMCP, DNM, D.C., is a leading functional medicine practitioner with a certification in natural medicine and a doctor of chiropractic degree.
Bone Broth
Image by Suzanne Clements / Stocksy
November 24, 2021

In the U.S., millions of people are living with an autoimmune disease, and that number only continues to rise.

Unfortunately, many people struggle with chronic, unexplained symptoms without realizing autoimmunity may be the cause. That's where my work comes in: In my telehealth functional medicine clinic, I have worked with countless patients, all of whom are on what I call "The Autoimmune-Inflammation Spectrum." One of the most important factors I consider with these patients? Diet.

My go-to diet strategy for autoimmunity.

Keto, paleo, carnivore, and GAPS are popular diets aimed at driving down inflammation and addressing the underlying dysfunctions contributing to autoimmune conditions.

The AIP diet (Autoimmune Protocol Diet1) is by far the most popular for autoimmune issues since it works to eliminate almost every single food that could potentially trigger inflammation for a minimum of 90 days before reintroducing foods at a set schedule to see what foods your body does well with.

In my book The Inflammation Spectrum, I walk you through my version of this plan, called Elimin8. In this plan, you spend eight weeks eliminating the following foods before reintroducing foods, one by one, while also leaning into an anti-inflammatory lifestyle:

  • Grains (even those without gluten)
  • Dairy products
  • Added sweeteners (ALL types, including stevia and monk fruit)
  • Inflammatory oils (corn, soy, canola, vegetable, etc.)
  • Legumes
  • Nuts and seeds
  • Eggs
  • Nightshades

After the reintroduction phase, most people are on their way to improving symptoms. Chances are, you'll know what foods cause you problems, and you'll have experienced relief in symptoms that should only continue after Elimin8. 

But for some people, that's not always the case, which can leave you frustrated and eager for answers. In reality, that just means you might have some less common sensitivities that we haven't pinpointed yet.

Potential sensitivities to consider.

Based on my experience, here are the additional sensitivities I look out for with patients:


Histamines are chemicals in your body produced in response to allergens. Your body produces white blood cells called mast cells to release histamines during the inflammatory-immune response to allergens. Histamine N-methyltransferase (HNMT) and diamine oxidase (DAO) are two enzymes that break down histamine. If there is a deficiency in these enzymes, one could experience histamine overflow or histamine intolerance. Histamine intolerance is essentially an allergic reaction without the allergen2, sometimes called a "pseudoallergy." The typical symptoms of histamine intolerance are similar to allergic reactions, such as rash, trouble breathing, and a runny nose, but they also include digestive problems or joint pain. Some high-histamine foods include:

  • Bone broth
  • Fermented foods (such as sauerkraut, kimchi, kombucha)
  • Cheese
  • Chocolate
  • Mushrooms
  • Nuts
  • Smoked meat
  • Spinach


This acronym stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols, or in short, fermentable sugars. The fermentation releases hydrogen gas that could lead to distention of the intestines, which can cause uncomfortable IBS symptoms in some people, such as pain, gas, bloating, constipation, and diarrhea. This would be considered a FODMAP intolerance and tends to be related to functional issues like small intestinal bacterial overgrowth (SIBO). Some FODMAP foods include:

  • Artichoke
  • Asparagus
  • Bananas
  • Cabbage
  • Garlic
  • Onion
  • Mushrooms
  • Sauerkraut
  • Legumes

"Moldy" foods

Certain types of mold release mycotoxins, or mold toxins3, that may contribute to inflammation. Some people with autoimmune issues may have trouble flushing these out, and it can exacerbate symptoms. Some foods that are high in mycotoxins (especially nonorganic versions) include: 

  • Rice
  • Coffee
  • Nuts
  • Dried fruit
  • Processed meat
  • Corn

Remember, wellness is a journey and shouldn't have a "one-size-fits-all" approach. If you are struggling with autoimmunity and have tried eliminating foods before, I encourage you to take it one step further and see if one (or a few) of these less common sensitivities might be contributing. Working with a doctor during this process is also encouraged. Your health is worth every single step it takes to get there!

Do you know what 3 health food myths are keeping you sick? Removing them from your diet is key for calming inflammation, healing your gut, and ditching fatigue & poor digestion for good. Register now for functional medicine expert Will Cole’s FREE webinar!
William Cole, IFMCP, DNM, D.C. author page.
William Cole, IFMCP, DNM, D.C.
Functional Medicine Practitioner

Will Cole, IFMCP, DNM, D.C., is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian,The Inflammation Spectrum, and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.