The autoimmune and gut-repair diet – Autoimmune diet

The autoimmune and gut-repair diet – Autoimmune diet

autoimmune protocol

autoimmune protocolMany people wonder what they can do immediately to manage their chronic health condition. The science can be confusing and complex, especially to those with Hashimoto’s hypothyroidism and other autoimmune diseases, because these disorders can lead to brain fog, fatigue, and loss of cognitive function that make it hard to figure out what to do next.

What people frequently fail to realize is that underlying all of these conditions is the most important foundation of all, and something you have the power to change right now — your diet.

In this article, I’ll give you the dietary basics for the autoimmune diet. The autoimmune diet is an effective diet and lifestyle protocol that helps autoimmune patients overcome the core underlying factors preventing recovery, including inflammation, leaky gut, hormone imbalances, blood sugar imbalances, micronutrient deficiencies, and immune system dysregulation.

The autoimmune diet is an elimination and reintroduction protocol: For a time you eliminate foods that are known to drive inflammation and resulting symptoms, and then you reintroduce foods methodically to rule out reactivity.

The optimal end result is a diet and lifestyle that support your health while avoiding factors that undermine it.

The diet must be very basic and simple so as not to trigger inflammation in the intestines and further worsen leaky gut and autoimmune flare-ups.

The literature identifies nutritional and herbal compounds that can facilitate your gut-repair progress. However, this diet is powerful therapy on its own.

The autoimmune diet focuses on these key areas

In any autoimmune condition, there are several key problem areas that underlie symptoms. The autoimmune diet seeks to address each of these, bringing the body back into balance so it can function properly.

  1. Gut health: Gut inflammation, gut dysbiosis (imbalances in gut bacteria), and a leaky gut lining contribute to poor absorption of nutrients and systemic inflammation that feeds the autoimmune response. In the diet, foods that irritate the gut lining are avoided, while foods that support gut health are included.
  2. Nutrient density: Every system in the body needs a wide array of nutrients to function at its best, including the immune system. Nutrient-dense foods are central to the diet, giving the body the tools it needs to heal deficiencies and support immune system function.
  3. Blood sugar balance: High and low blood sugar can lead to systemic inflammation, immune flares, hormonal imbalances, and compromised brain function. Supporting balanced blood sugar is critical for recovery from any inflammatory condition. The autoimmune diet gives you the tools to support healthy blood sugar balance.
  4. Immune system regulation: Inflammation, leaky gut, hormone imbalances, blood sugar imbalances, and micronutrient deficiencies all contribute to immune system dysregulation. By reducing bacterial overgrowth and inflammation in the gut, removing food-borne immune triggers from your diet, providing dense nutrition and supporting blood sugar regulation, the autoimmune diet helps to support healthy immune function.

Tips for using the autoimmune diet

autoimmune gut-repair diet

autoimmune gut-repair diet

These are always good basic guidelines with which to start whether you are waiting to work with a practitioner or are going it alone:

  • Focus on eating 6-9 servings of vegetables per day, including the full color spectrum. For more information on why plenty of vegetables is so important, please see my course on oral tolerance.
  • Eat plenty of essential fatty acids (ideal omega-6 to omega-3 ratio is between 1:1 and 4:1).
  • Eat plenty of fermented foods to support healthy gut flora.The exception may be if you have a histamine intolerance.
  • Make sure you don’t allow yourself to get too hungry or hypoglycemic, by including sufficient appropriate fats and protein in your diet.
  • Eat frequently enough to avoid energy crashes caused by low blood sugar
  • Stay hydrated with plenty of fresh, filtered water. Also, cravings are often a disguise for thirst, so stay hydrated and add electrolytes to your water if need be.
  • Strictly avoid foods on the “Foods to avoid” list. Even just a bite of these foods can trigger an immune reaction, inflammation, and an autoimmune flare-up. Cravings for these foods will pass quickly, especially as you start to feel and function better.
  • For this diet to be successful it’s extremely important to pay attention to blood sugar symptoms, keep blood sugar stable and be aware of which foods trigger your symptoms.
  • Elimination/Reintroduction: This protocol is intended as a elimination diet to quell inflammation, then a reintroduction period to determine food sensitivities and know the best foods for you.

Important daily lifestyle habits to support your healing

  • Get enough sleep to avoid inflammation.
  • Manage stress: What stressful factors can you reduce or eliminate from your life? What daily stress-reducing activities can you engage in?
  • Exercise: Avoid over exerting yourself. High-intensity interval training shows great benefits for dampening inflammation, however any sort of regular physical activity is better than none. The exception may be severely brain-compromised people whose symptoms are triggered by exercise. Use trial and error to find what works for you.
  • Maintain social connections: Many studies show that those who maintain healthy social connections are healthier, happier, and live longer.

Foods to eat

When considering this diet, the first thing people ask is what can they eat. In fact, you’ll be eating the way people ate for most of human history — there’s plenty of food that doesn’t come from a factory or an industrialized farm. Of course, if you have an intolerance to any of these foods, don’t eat it just because it’s on this list.

autoimmune gut-repair dietautoimmune gut-repair diet

Most organic vegetables: Include as much variety as possible, making sure to include the full color spectrum.

Quality meats: If possible, select hormone-free, antibiotic-free, and pastured meats.

Organ meats and offal: Organ meats provide concentrated forms of nutrients.

Glycine-rich foods: Include foods containing connective tissue, organ meat, joints, skin, or bone broth.

Fish and shellfish: Seek out ocean-caught cold water, low-mercury fish with high fat content. Swordfish, most tuna, and king mackerel are very high in mercury.

Quality fats: Choose pasture-raised, grass-fed animal fats, fatty cold water fish, olive oil, avocado oil, coconut oil, and low-mercury Omega 3 supplements.

Low glycemic organic fruits: Eat fruits lower in sugar and eat them with fat, fiber, or protein to slow the uptake of sugar.

Edible mushrooms: Mushrooms are generally fine for most individuals. However, some people with autoimmune conditions may react to immune-stimulating fungi such as Maitake and mushroom-derived beta-glucan, so monitor your response.

Probiotic and fermented foods: Fermented foods include sauerkraut, kimchi, fermented pickles (not packed in vinegar), coconut yogurt, kombucha, water kefir, and coconut milk kefir. You may need to make your own or buy one of the few brands that are genuinely fermented and free of sugars or additives. Also, search for information about anaerobic fermented foods in air-tight containers that do not produce histamines if you have histamine intolerance.

Coconut: Enjoy coconut and coconut products that are free of sugars or additives.

Noodles: Shirataki yam noodles (sold in Asian grocery stores and some natural food stores) are a good source of fiber, but avoid the noodles that contain tofu (soy).

Herbs and spices: Avoid herbs and spices that are nightshades. Good options include basil, cilantro, cinnamon, clove, garlic, ginger, horseradish, lemongrass, mace, mint, oregano, parsley, rosemary, sage, saffron, sea salt, thyme, turmeric.

Vinegars: Avoid grain-based vinegars and instead choose apple cider, balsamic, champagne, coconut, red wine, sherry, ume plum, or white wine vinegars.

A note on fatty acids: Consuming a proper ratio of omega-6 to omega-3 fatty acids is key for minimizing inflammation in the body. Too much omega-6 is highly inflammatory, so it’s important to get enough omega-3 to compensate. The average American ratio is close to 25 parts omega-6 to one part omega-3, resulting in high levels of inflammation. Researchers recommend a ratio of omega-6 to omega-3 fatty acids that ranges from 1:1 to 4:1 for optimal health and prevention of disease. Supplement your diet with plenty of fish oil.

Foods to avoid

  • Grains
  • Beans and legumes: This includes products made from peanuts and soy, which are legumes.
  • Nuts
  • Seeds
  • Seed-based spices: These include anise, annatto, celery seed, coriander, cumin, fennel, fenugreek, mustard, nutmeg, poppy seed, sesame, allspice, star anise, caraway, cardamom, juniper, peppercorns, sumac, whole vanilla bean.
  • Dairy: This includes dairy from sheep or goats and raw dairy.
  • Eggs
  • Nightshades: Nightshade vegetables include eggplant, goji berries, sweet and hot peppers, hot pepper sauces, tomatillos, tomatoes, and white potatoes.
  • Nightshade-based spices: These include cayenne, chili powder, paprika, red pepper, and curry.
  • Medicinal mushrooms: Some people with autoimmune conditions may react to immune-immune-stimulating medicinal mushrooms.
  • Refined and processed oils and vegetable oils
  • Sugars and sweeteners, including natural ones
  • Artificial sweeteners
  • Emulsifiers, thickeners, and other food additives: Watch out for guar gum, carrageenan, xanthan gum, cellulose gum, soy lecithin, and other additives.
  • Alcohol
  • Hidden sources of gluten: Always read the labels as gluten is hidden in many foods and additives. Beware of non-specific ingredients such as “natural flavorings.”
  • NSAIDS: Non-steroidal anti-inflammatory drugs such as aspirin and ibuprofen inflame the gut so avoid if possible.
  • Other: Avoid canned foods, processed foods, wheat grass, barley grass, brown rice protein, pea protein, hemp protein, licorice root (DGL is okay), aloe, slippery elm bark, commercial egg replacers, supplements containing ashwagandha (a nightshade) or oat seed, and immune stimulants such as chlorella and spirulina.

Elimination and reintroduction of foods

The autoimmune diet is an elimination and reintroduction protocol. After eliminating foods that trigger inflammation for a period of time, you then reintroduce each food one at a time every three days to rule out reactivity.

Wait until you notice a significant improvement in your symptoms and quality of life before reintroducing foods, which varies for each person. If you begin reintroducing foods while you are still symptomatic, you will not be able to gauge whether a reintroduced food is causing a reaction.

If you notice symptoms when you reintroduce a food, avoid that food, return to the autoimmune diet, and wait for symptoms to subside before reintroducing the next food. Symptoms vary and can include digestive upset, mood changes, fatigue, pain, sleep issues, brain fog, skin rash, or respiratory issues.

IMPORTANT: If you have a reaction to a food reintroduction, you must wait until those symptoms are completely gone before moving on to the next reintroduction.

Lectins in grains and legumes

Grains and legumes are high in proteins called lectins. Lectins have been shown to degrade the intestinal barrier, adding to leaky gut. They can also be transported through the damaged intestinal wall into the bloodstream, where they may bind to insulin receptors and leptin receptors. Some believe lectins may also have the ability to desensitize these receptors, thus contributing to insulin resistance and leptin resistance.

When transported through the gut wall into the blood stream, lectins can also set off an immune reaction that further damages the intestinal wall and sets off systemic inflammation, further supporting the autoimmune reaction.

Molecular mimicry: some foods can cross-react with gluten

Grains, legumes and some other foods present problems for other reasons. Research has shown that many gluten-intolerant people cross-react with other foods. In other words, their body erroneously recognizes other foods as gluten and reacts with an immune response that destroys not only the food proteins, but bodily tissue.

Not surprisingly, most grains fall into the category of top 24 foods most often to cause cross-reactivity, including amaranth and quinoa.

Other common cross-reactive foods include dairy, chocolate, sesame, and instant coffee. Fortunately it is now possible to test which foods might be provoking a cross-reaction to gluten, which you can read about here.


I tell all my gluten-free patients to avoid corn, even though this contradicts the advice on many gluten-free websites. The protein in corn is similar enough to that in wheat and wheat-like grains that it can provoke an immune response. Also, corn has been bred over the years to resist pests. Unfortunately, this bred into corn a compound called fucosamine, which is carcinogenic.

Seeds and nuts

Tree nuts are one of the top allergens and food sensitivities. Leaky gut is exceedingly common in autoimmune patients, and it increases the likelihood of developing food allergies and sensitivities. By removing seeds and nuts from the diet during elimination phase, one is better able to determine if a sensitivity exists.

In addition, the fiber in nuts and seeds can contribute to gut irritation.


Nighshades contain digestion-resistant and gut-irritating lectins, saponins, and capsaicin (a steroidal stimulant) that can contribute to leaky gut and pass through the gut lining, contributing to inflammation.

Addressing subconscious beliefs about food

For those battling a history of weight issues or an eating disorder, this diet can be filled with emotional triggers. In these cases, I highly recommend support for underlying subconscious beliefs about food, eating, and your body. Ideas include hypnotherapy, emotional freedom technique (EFT) workshops or instruction, guided meditations and visualizations. You will find plenty of instruction online.

Subconscious beliefs aside, many are pleasantly surprised to find cravings and obsessions with food diminish or disappear once they remove immune reactive foods, stabilize blood sugar, and eat a nutrient-dense diet.

Autoimmune diet resources and ongoing support

The autoimmune diet can seem daunting at first, and planning is essential to success. Fortunately, ample support exists on the internet today for the autoimmune diet.

You must have the right foods on hand at all times. It’s helpful to batch cook so you have meals at hand and are not tempted to fall off the wagon. Look for recipes compliant with the autoimmune diet on my website or in my courses.

To learn more about how to manage autoimmunity, please see my 3D Immune Tolerance Program and Save Your Brain courses.

I also suggest my book  Why Isn’t My Brain Working? to learn about ways your brain plays a role in your gut and immune health.


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