Top 6 Autoimmune Triggers: Start With Food

“An estimated 99 percent of people who have a problem with eating gluten don’t even know it. They ascribe their ill health or symptoms to something else–not gluten sensitivity, which is 100 percent curable.”

— Mark Hyman, MD and founder of the Center for Functional Medicine at the Cleveland Clinic

Environmental factors — that is, anything you put in or on your body or absorb from your environment — account for about 90-95% of the autoimmune equation. Your genes only contribute maybe 5-10% of the risk!1 Turns out the food you eat everyday has a profound influence on your risk for autoimmune conditions.

To prevent or heal from an autoimmune disorder, you’ll need to identify your personal triggers so you can eliminate them or minimize your exposure. I categorize the top 6 major autoimmune trigger categories as:

Top 6 Autoimmune Triggers: Food

When it comes to healing from an autoimmune disorder, food and dietary components (e.g., food additives, preservatives, and chemicals), offer the biggest bang for your buck. Just removing your trigger foods can go a long way and sometimes ALL the way to help you reverse and/or prevent autoimmune conditions.

The Before-and-After Stories are Powerful:

  • I completely eliminated gluten and dairy in 2010 after discovering I had non-celiac gluten sensitivity (NCGS) and a sensitivity to casein–an inflammatory protein found in animal dairy, especially dairy from “A1 cows” like Holstein.2 I have never had another Multiple Sclerosis (MS) symptom since.
  • Linda Clark, M.A., CNC eliminated her food triggers: gluten, grains and dairy, and went Paleo for good. As a result, all of her symptoms vanished and she has been free of multiple autoimmune diagnoses: multiple chemical sensitivities (MCS), fibromyalgia (FM), chronic fatigue syndrome (CFS), Hashimoto’s thyroiditis, and celiac disease.
  • One of the most compelling “food as medicine” stories is that of Terry Wahls, MD, a clinical professor of medicine and scientist who reversed her progressive MS by removing gluten, dairy and eggs and adding copious amounts of nourishing foods and supplements.

It can be daunting to contemplate the dietary changes that are usually needed in order to reverse your autoimmune condition(s). But, many have done it with astonishing results. Once you experience freedom from symptoms by removing your food triggers you may never look back!

Autoimmune Trigger Foods

The top 10 trigger foods cause lots of immune system problems and occasional digestive distress. Not surprising, since 75% of our immune system resides in the lining of our guts! Problems with the top 10 autoimmune trigger foods include gut inflammation, imbalances in gut flora (dysbiosis), tears in the one-cell-thin lining of the intestines (“leaky gut”), nutrient deficiencies, and immune system impairment. Beyond the gut, these inflammatory foods are directly linked to mood disorders, migraines, joint pain, fatigue, skin issues, and even dementia.

You don’t absorb foods well if your gut is leaky. And, if you’re over 40, chances are good that you don’t create enough stomach acid and digestive enzymes to break down the food you eat. Consider taking 500 mg HCL (hydrochloric acid) with pepsin and digestive enzymes with meals. If you have the genetic predisposition for autoimmune disease, a leaky gut puts you on the fast track to autoimmunity.

Often these foods do damage without causing obvious digestive distress or immediate symptoms, which makes them stealthy triggers. Unfortunately, the biggest culprits are often the foods we eat the most – even if those foods are not normally “toxic” — like tomatoes, nuts, and eggs.

The biggest question I get is What should I eat to beat an autoimmune condition?! I created Eat to Beat Autoimmune: Your Optimal Food Guide, a free e-book to help you find YOUR best foods.

Remove the Top 10 Autoimmune Trigger Foods


A 2002 review in the New England Journal of Medicine, arguably the most well-respected scientific journal, lists 55 diseases that can be caused by eating gluten, including osteoporosis, inflammatory bowel disease, anemia, cancer, rheumatoid arthritis, lupus, multiple sclerosis, and many other autoimmune diseases.3 More recent research shows that gluten creates a leaky gut in anyone who eats it. Read more HERE.


Drinking cow’s milk has been associated with an increased risk for numerous autoimmune diseases including multiple sclerosis, rheumatoid arthritis and Type 1 diabetes.4 If you have trouble with cow dairy, replace butter with ghee — clarified butter, which is delicious and casein free!


If you are dealing with gut inflammation, leaky gut and autoimmune issues, eggs, especially egg whites, could make symptoms worse. Egg white (protein) can permeate the gut lining and cause the immune system to react even more. Remove all eggs for one month to identify whether they are a trigger for you. 5

Cross-Reactive Foods

People sensitive to gluten (which may be a third of the population) must also consider eliminating “cross-reactive” foods. Cross-reactive foods are foods that the immune system mistakes for gluten. They include milk chocolate, instant coffee, all cereal grains, corn, rice, yeast, millet and milk.6


There are a number of problems with grains. They often contain gluten; they are often genetically modified; they are frequently sprayed with glyphosate (herbicide) prior to harvesting; they can be tough to digest; they are high in carbohydrates, which can elevate blood sugar and insulin; and they can “cross-react” with gluten — meaning they cause an immune response in people sensitive to gluten. Cross-reactive grains include: rye, barley, spelt & kamut®, oats, millet, corn, and rice.7


Sugar in all its forms (glucose, fructose, and sucrose) weakens the ability of white blood cells to destroy biological agents. This weakening begins within a half hour of eating sugar and lasts for 5 hours. After 2 hours, immune function is reduced by 50%.8

Processed Foods

The Standard American Diet (“SAD”) is filled with packaged, processed foods loaded with hydrogenated (chemically altered) oils, high fructose corn syrup, artificial sweeteners, transfats, refined grains and sodium chloride (processed white table salt). SAD foods promote obesity, metabolic syndrome, diabetes, cardiovascular disease and susceptibility to autoimmune disorders.9

White Table Salt

Too much refined and processed salt* may be one of the environmental factors causing an increase in autoimmune diseases. Mice fed a high-salt diet showed a dramatic increase in the number of Th17 cells that cause inflammation and disease in their nervous systems.10 *Note: We are referring to white table salt — which contains sodium chloride among other chemicals, iodine, preservatives & sometimes sugar — not sea salt.


Lectins are a sticky protein plants use to defend themselves from being eaten by insects — or us. Problem with lectins is they are difficult to digest, stick to the lining of your intestines, create imbalanced gut flora and a leaky gut. Foods highest in lectins include beans, legumes (includes lentils, peanuts and peas), grains and nightshade vegetables. Cardiologist and health educator Steven Gundry, MD says, “My research and others suggest that lectins cause most heart disease, arthritis, dementia, diabetes and all autoimmune disease.”11 12

Tree Nuts

Tree nuts are one of the top allergens and most common food sensitivities. People with autoimmune disorders are more likely to have a sensitivity or allergy to nuts (and seeds) than other people. Remove nuts during the elimination diet to isolate whether or not nuts are a problem for you.13

What You Can Do: Detect, Remove, Repair

  • Detect

    Here are two good options to figure out what if any foods or dietary components are causing you harm:

a. Take a 30-Day Food Vacation. Many holistic and functional docs agree that a comprehensive elimination diet is the “gold standard” when it comes to discovering which foods are causing your immune system to overreact. I’ve rebranded it as a 30-Day Food Vacation, because eliminating things sounds so negative; and during this time you can explore and experiment with many new foods. Studies show elimination diets are extremely effective in reducing or completely eliminating symptoms.14 Remove gluten, grains (corn, rice, and oats too!), sugar, dairy, eggs, legumes (soy, lentils, beans and peanuts), nuts & seeds, nightshades (i.e., tomatoes, white potatoes, peppers, eggplants, and goji berries), alcohol, and coffee for at least 30 days, or until your symptoms fade or disappear. Go slow with reintroducing foods, one at a time, and at least 48 hours apart. Pay close attention to how you feel. Do you have headaches, brain fog, more tingling, a tummy ache, gas, etc.? Your body will talk to you; you just need to listen.

b. Get Tested. 

Three of my favorite labs that offer comprehensive gluten and other food sensitivity tests are Vibrant Wellness, Cyrex Labs and ELISA/ACT®. 

  • Remove

To heal, you must eliminate the foods triggers you identified in the Detect phase. For those with gluten sensitivities and any autoimmune concerns – not just celiac disease — gluten needs go for good.

After the elimination phase you can reintroduce other suspect foods one at a time and slowly to see if you react. Remove highly reactive foods for 6 months. This will give your immune system a chance to settle down and time for you to heal and seal your gut.

  • Repair

a. Heal and seal your leaky gut by removing inflammatory factors, sipping bone or meat broth, and taking targeted supplements that repair the gut lining. Gut healing supplements include: L-glutamine powder, zinc, pantothenic acid (vitamin B5), vitamin A, licorice root (DGL), aloe vera juice (inner aloe plant filets), and essential fatty acids.

b. Tend to the balance of your gut bacteria with probiotics (beneficial bacteria), prebiotics (fiber that feed the probiotics), fermented foods, and a variety of colorful vegetables.

c. Nourish your body with nutrient-dense, anti-inflammatory foods, emphasizing above-ground vegetables. Choose organic whenever possible. Concerned about cost? Visit The Environmental Working Group (EWG) to see which fruits and vegetables made the Clean 15 and Dirty Dozen yearly lists.

The Science of Nourishing Foods & Supplements

  • Green Tea

    Green tea contains many beneficial compounds. One of these, a polyphenol called EGCG, has a powerful ability to increase the number of “regulatory T cells” that play a key role in immune function and suppression of autoimmune disease.15 Note: Some people — those with lupus, ulcerative colitis and/or genetically don’t deal well with green tea. 

  • Saturated Fats

    Consuming healthy saturated fats in the form of coconut, organic, pastured meats, ghee and pastured lard can help ease inflammation, strengthen your bones, improve lung, liver and brain function, improve cardiovascular risk factors, modulate nervous system function, and strengthen immune system function.16 Note: Saturated fats may not be as beneficial for people with SIBO (Small Intestine Bacterial Overgrowth) and/or celiac disease. 

  • Extra Virgin Olive Oil

    Extra virgin olive oil turns off multiple inflammatory genes that are activated as a consequence of metabolic syndrome. This effectively provides a protective shield against cardiovascular disease and other chronic illnesses driven by persistent inflammation. NoteRancidity is a huge concern with olive oil. Look at the harvest and bottling dates and make sure you are consuming as close to those dates as possible.17  

  • Curcumin

    Curcumin (from turmeric root) is a powerful anti-inflammatory with far-reaching benefits, as evidenced by numerous studies.18 Curcumin is beneficial for multiple sclerosis, rheumatoid arthritis, psoriasis, and inflammatory bowel disease.19 You can cook with it, make tea with it, and/or take supplements. Just make sure you add some black pepper (piperine) for best absorption. Start with 250 – 500 mg per day.

  • Omega-3 Essential Fatty Acids (EFAs)

    Supplementation with omega-3 essential fatty acids (EFAs) can alleviate many symptoms of autoimmune disease through their anti-inflammatory activity. EFA’s are abundant in fish, flaxseed, borage oil, evening primrose oil, and blackcurrant seed oil. 20 Note: It’s ideal to get your omega-3 oils from small and wild fish, like sardines and salmon. If you do buy capsules, check for purity and best extraction processes. Three of my favorite brands include OmegaBrite, Nordic Naturals and Carlson Labs.

  • Dietary Polyphenols

    Berries — including blackberries, blueberries, raspberries, sour cherries, pomegranates and cranberries — are especially rich in polyphenols, powerful antioxidants and anti-inflammatories. Studies done on different human populations have shown that those who consume polyphenol-rich foods have lower incidences of inflammatory disease.21 Note: If you have blood sugar or insulin issues like diabetes, minimize or avoid fruit until your insulin sensitivity is restored.

  • Cultured Super Foods

    Regular consumption of cultured super foods like sauerkraut, goat or coconut kefir and yogurt introduces beneficial microbes into the digestive tract to aid digestion and detoxification, provide enzymes, vitamins and minerals, and boost immunity.22

  • White Peony Root

    In numerous scientific studies, peony glucosides from the root of the white peony flower, have been demonstrated to significantly and meaningfully restore immune system balance, reduce symptoms, speed onset of remissions, and reduce the amount of dangerous immunosuppressive drugs required.23Note: White peony is lighter than green tea and has a more delicate flavor.

  • Quercetin

    Quercetin, an antioxidant that’s found in apples, leafy greens, berries, and broccoli enhances intestinal tight junctions, strengthening the gut barrier.24

  • Micronutrients: Selenium, Zinc & Magnesium

    People with autoimmune conditions are often deficient in micronutrients including selenium, magnesium and zinc. Brazil nuts are high in selenium, which is essential for healthy thyroid function.25

Follow these three powerful steps: Detect, Remove and Repair and you’ll be well on your way to reversing and preventing autoimmune conditions.

Have you made the connection between food and autoimmune symptoms? If you haven’t yet figured out your food triggers, I’m excited for you to try the elimination diet. Give yourself at least 30 days and commit to doing it 100%.

Once you feel freedom from autoimmune symptoms, you’ll likely realize that nothing tastes as good as feeling healthy feels.

Take very good care!

P.S: Want my help reversing an autoimmune condition?

Want my help beating an autoimmune condition and optimizing your immunity? If you live the U.S. and are ready, willing, and able to invest in your best health, I offer Functional Medicine Total Health Transformation Programs over Zoom. I collaborate with a naturopath who is an expert in resolving chronic infections and toxic burdens which are almost always part of the autoimmune puzzle. Together we provide comprehensive, customized treatment plans, and collaborative, caring support. Sign up for a complimentary 30 min discovery and strategy call to discuss your health challenges and goals. If you’re truly ready to invest in your best health and life, I’d love to talk with you.




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Palmer is a certified Functional Medicine Health Coach who has helped thousands of people reverse autoimmune conditions based on her own two-decade battle to successfully beat multiple sclerosis (MS). She’s the author of the Amazon #1 bestselling book, Beat Autoimmune, which has a powerful foreword by Functional Medicine pioneer, Mark Hyman, MD.

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