Autoimmune Diet

Autoimmune Diet: Foods & Supplements Considerations for Autoimmunity

Dr. Jennifer Kessmann MD IFMCP Dr. Jennifer Kessmann, MD
Functional Medicine Doctor
Autoimmune Diseases Expert

Foods to Avoid | Foods to Eat | Foods Rotation | Supplements
Sixty to seventy percent of the immune system resides in the gut. So, it should be no surprise that more and more research is finding that autoimmunity may actually begin in the digestive tract.

Whether the trigger is food sensitivities, a compromised gut flora or microbial imbalances like candida and yeast overgrowth, your diet can help control potential immune triggers.

In this article, Dr. Kessmann covers some of the key guidelines and considerations for the autoimmune diet that can help you manage your autoimmune symptoms to improve quality of life. The information in this article is meant to educate you about the various dietary options for autoimmunity and help you discuss the best treatment plan with your doctor.

Related post: Functional medicine approach to autoimmune diseases.

Autoimmune Diet – Foods to Avoid

Autoimmune Diet - Foods to Avoid

It is very important to eat organic whenever possible. GMOS and pesticides are foreign substances to our immune system. The has a list of the most sprayed foods that should always be eaten organic due to high amounts of pesticides.

While the autoimmune diet should always be tailored based on your individual needs, below are some of the common guidelines:

The Elimination Diet

A key dietary concept in functional medicine known as the elimination diet can be very helpful in autoimmunity. With this approach, you stop eating foods that are most likely to trigger an immune reaction for at least six weeks.

After improvement, you reintroduce each food, one at a time. If you notice a reaction, you are likely sensitive to that food and should avoid it.

The most common reactive foods include:

  • Gluten
  • Dairy
  • Soy
  • Corn
  • Nuts (especially peanuts and tree nuts)
  • Shellfish
  • Nightshades (such as peppers, tomatoes, eggplants), especially important in rheumatoid arthritis diet
  • Eggs
  • Beef (see options for meat in the next section)
  • Sugars (can amplify microbial imbalance such as candida).

Based on your individual food sensitivity test results, you may need to eliminate other “less common” foods.

Foods to Eat

Autoimmune Diet Foods to Eat

Probiotic & Prebiotic rich foods

The healthier your gut bacteria, the less active your immune system will be in the gut. Fermented foods such as yogurt, kimchi, and sauerkraut, are high in healthy bacteria called probiotics that can help promote gut health and calm the overactive TH17 immune system.

Prebiotics are a type of fiber that serves as a fuel source for probiotics and therefore, can support the growth of healthy bacteria in the gut. Good sources include: asparagus, dandelion greens, garlic, and other green vegetables.

Antioxidant-rich Fruits & Vegetables

Plants contain protective compounds called phytonutrients that help them resist threats from the environment such as sun radiation, mold and bacteria. When we eat the plants, we also get these protective benefits.

One of these important nutrients, called antioxidants, can help reduce oxidative stress caused by the overreactive immune system. Each plant color is representative of a different antioxidant and health benefits. To get the most variety of nutrients and benefits, you should eat a rainbow of colorful fruits and vegetables.

Beta-carotene, the red-orange pigment found in sweet potatoes and carrots for example, can support a healthy Th1-Th2 cell balance that plays a key role in the immune response.

Try to include cruciferous vegetables such as broccoli, cauliflower, brussels sprouts and kale. These are high in sulfur-rich compound called sulforaphane that can promote healthy Th1 cell activation which helps with viral infections.

Animal Proteins

Commercial meat and seafood is often contaminated with toxins and heavy metals that can trigger an immune system response. When you eat animal products, you are also consuming what the animal ate, which may include toxins from its environment.

To minimize these issues, look for organic grass-fed beef, pasture-raised chicken, turkey or lamb. For fish (up to twice a week), best options include wild caught small fish with low mercury content such as salmon, sardines and anchovies. Farm-raised fish are often fed with foods that are not meant to be consumed by fish and should be avoided.

Healthy Fats

Having enough good fats in your diet such as cold-pressed organic extra virgin olive oil and fish oil can help modulate inflammation that is often a problem with autoimmunity.

Avocados, sprouted pumpkin seeds and coconut oil are generally good options and may be ok for most people. They may however cause issues for others.

This is one of the reasons that the autoimmune diet should always be tailored to the individual. With the overreactive immune system, many foods (even healthy ones) can cause an immune reaction and should be rotated. The more variety the better.

Herbs & Spices

Certain herbs and spices can help inhibit immune system promoters such as NF-κB which are often activated during autoimmunity. You can add these to your foods, or in some cases, use as supplements.

Generally speaking, getting these herbs and spices through the diet is optimal. They can calm down the over reactive immune system, without overdoing it. With NF-κB inhibitors, more is not better. You still want the immune system to be effective and respond to infections and other threats.

Common examples of natural NF-κB inhibitors include ginger, garlic, turmeric, ashwagandha, holy basil, milk thistle and thyme.

Another reason to add more herbs and spices to your foods, is that some of them can also modulate inflammatory Cox1/Cox2 enzymes.

So if you enjoy adding ginger, turmeric, garlic to your meals, it may be a good idea to do so presuming you are not allergic to them. Other natural options that can help control inflammation include fish oil and quercetin (found in apples and cherries).

Rotate Your Foods Every Four Days

In addition to the foods you eat and avoid as a part of the autoimmune diet, food rotation is a powerful concept that can help limit reactions to different foods.

When the overactive immune system is out of control, many foods, even those that are considered healthy, can cause an immune reactions. This amplification of the immune system may last up to three days after you eat the foods.

So if you eat blueberries for breakfast on Sunday, the immune reaction may last until Wednesday. This can become a problem if you keep eating blueberries every day if you are reacting to them.

By rotating your foods every four days, you decrease the immune system reactivity to specific foods and lower your risk of immune system amplification from eating the same things over and over.

Autoimmune Supplements

Autoimmune Diet & Supplements

Just like the autoimmune diet, the exact protocol may vary from one person to another. With that said, here are the most common supplements that can be very helpful for autoimmune diseases:

Vitamin D

Having adequate levels of vitamin D can support the T-regulatory cells that help moderate the immune system. Make sure your vitamin D levels are between 50-80 ng/mL to maintain a healthy active immune system. This is especially important considering that vitamin D deficiency is an epidemic.


In addition to probiotic-rich fermented foods, probiotic supplements are a mainstay of autoimmune disease treatment due to their ability to calm down the immune system activity in the GI tract and decrease reactivity to foods.

Healthy bacteria in the gut can also help control microbial imbalances like candida yeast, which can cause an immune reaction.

Ideally, you should rotate your probiotic supplements with multiple probiotic strains to help support the growth of a diverse microbiome. Look for strains that are refrigerated with the number of live cultures mentioning on the label.

Fish oil

Omega 3’s fatty acids in fish oil can help to reduce inflammation and balance the pro-inflammatory omega 6 levels that are way too high in the Western diet. Make sure the oil you use is from a trusted source that guarantees it is free of heavy metals and other toxins found in fish.

Omega 3 dose may be different based on the individual. Many of the studies that have been done with fish oil that did not show benefit were done with doses that were below the effective amount. It is important to understand the source of information and not get side tracked by inaccurate data. Also, the quality of the supplement is important.

Other useful supplements include:

  • Glutathione & NAC:
    Can help to calm the immune system, decrease oxidative stress, support t-regulatory cells, and improve the body’s ability to detoxify. Eliminating toxins effectively is important as these can trigger an immune response.
  • B vitamins:
    Essential for maintaining essential cellular processes and healthy detoxification.
  • Natural NF-κB inhibitors (when needed)
    Such as Resveratrol and Curcumin.
  • Well-balanced multivitamin:
    To help bridge potential nutritional gaps that can worsen autoimmunity.
  • Magnesium and minerals:
    Magnesium is used in so many vital biochemical reactions in the body and is deficient in most foods.

Read Next

Functional medicine approach to autoimmune diseases: Dr. Kessmann discusses key natural lifestyle and dietary steps that can help with autoimmunity.

Dr. Jennifer Kessmann, MD, AIHM, IFMCP

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