Top Foods To Eat If You Have An Autoimmune Disease

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Science is starting to show more and more that the dietary choices you make when suffering with an autoimmune disease can either help or hinder your health. Food won't cure your autoimmune condition, but it can help put it into remission (like celiac disease) or it can help relieve debilitating symptoms. 

Eating foods that are rich in nutrients and free of contaminants (like pesticides) and correcting nutrient deficiencies will benefit your health. This is especially important in autoimmune disease because many medications that are used deplete the body of nutrients. The focus when choosing helpful foods should be to identify and eliminate inflammatory foods and nourish with real foods that deliver vitamins, minerals, and antioxidants. 

So what are some important foods to eat to resolve those nutritional deficiencies, nourish your body and support overall health? 

Healthy Fats
Autoimmune diseases emerge when the immune system mistakenly attacks healthy cells. The exact cause of such physiological slip-ups is still unclear, but researchers are now beginning to learn that dietary fats could influence how these symptoms present themselves. Not all fats are created equal, some are pro inflammatory and others are not. Trans fats result in poor health and inflammation while omega 3 fatty acids can turn down your bodies inflammation. 

Short-chain fatty acids, typically found in fiber-rich diets, are only metabolized by gut bacteria. Omega-3 fatty acids are made of short chain fatty acids like in fish, nut and seeds. Since many autoimmune conditions are thought to originate in the gut and gut health is directly linked to autoimmune symptoms, eating omega 3 fatty acids is very important if you have an autoimmune condition. 

A research team discovered that giving the mice short-chain fatty acids promoted the growth of regulatory T cells, which help keep the immune system in check. They ended up improving the disease in the animals. (1)   

What foods to eat to get healthy fats
Increase your omega-3 intake by eating more wild caught fish (canned salmon and sardines are great inexpensive options), omega-3 eggs, and maybe also using a good quality fish oil supplement. It is also important to reduce your intake of omega-6 fatty acids to the best of your ability (and budget).  This means no modern vegetable oils or products made from them, like mayonnaise or store-bought salad dressings.  Also, be mindful of your nut consumption and try to eat grass-fed meat, free-range poultry, and wild game whenever possible. 

You have probably heard of probiotics, but what are prebiotics and what do they have to do with autoimmune disease? As I touched on earlier the health of your gut is directly correlated to your autoimmune condition. Poor gut health and autoimmune disease (especially digestive autoimmune disease) go hand in hand. So feeding your body foods that support and nourish your gut health is key for transforming your health. 

“Prebiotics” is a catch-all term that refers to all the different kinds of fiber that encourage beneficial species of gut flora to grow. You can’t digest them, but your gut flora can – and more food for the gut flora means more flora. Prebiotics are not the same thing as probiotics:

  • PREbiotics provide food for the bacteria already living in your gut.
  • PRObiotics provide a direct infusion of bacteria that weren’t there before.

Prebiotics are probably already in your diet; you just didn’t realize it.

Some foods high in prebiotic fibers include:

  • Dandelion greens
  • Garlic and onions (and any vegetables in that family, e.g. leeks)
  • Asparagus
  • Bananas
  • Chicory (used in coffee substitutes)

It's important to note that probiotics are great but not for everyone. In some prebiotics can sometimes do more harm than good:

  • People with Small Intestinal Bacterial Overgrowth (SIBO) often find that prebiotics are the exact opposite of what they need (if you already have too many bacteria, feeding them even more is not going to help).
  • Many people with Irritable Bowel Syndrome or FODMAPs intolerance find that prebiotics make their symptoms worse.

So if you have or suspect these conditions then avoiding prebiotics is best, but for others these food can be helpful. 

Probiotic Foods
While the research into the role specific bacterial strains play in our body is on-going, we do know that eating fermented foods on a regular basis is beneficial when addressing autoimmune disease. A healing addition to your diet, they are involved in immune modulation; fighting infection; speeding the healing process; have anti-inflammatory effects; and provide digestive benefits such as improving the integrity of the gut wall, and helping to correct gut dysbiosis (an imbalance in gut bacteria).

Not only is it a good idea to eat fermented foods to ensure you get the good microbes into your gut but also so that you keep the bad ones out. Dysbiosis is a microbial imbalance on or within the body or an overgrowth of ‘bad’ microbes which can lead to health issues. I put bad within in commas because we all have a little bit of the ‘bad guys’ in our gut, and that is okay. It becomes a problem only when they get out of control and outnumber the ‘good guys’.

Foods high in probiotics:

Fermented Vegetables

  • Pickles (cucumbers)
  • Sauerkraut (cabbage)
  • Kimchi (cabbage and other veggies)
  • Capers (flower buds of Capparis spinosa, a shrub like bush)
  • Olives

Fermented Dairy

  • Yogurt
  • Kefir


  • Kombucha

If you with a histamine sensitivity you may have problems with many fermented foods, but before you give up, try kombucha which is known to be better tolerated. If you have a yeast sensitivity, you may only use probiotic supplements because while fermented foods are known for their beneficial bacteria, they also contain beneficial yeasts that can cause a reaction.

Fruits and vegetables contain an many antioxidants and other disease-fighting compounds that are very difficult to get anywhere else. Plant chemicals called phytochemicals can reduce inflammation and eliminate carcinogens, while others regulate the rate at which your cells reproduce, get rid of old cells and maintain DNA. 

We know that inflammation goes hand in hand with autoimmune disease. During an immune response, there’s an increase in the production of free radicals, which can result in oxidative stress (a negative shift in the natural balance between oxidants and antioxidants that results in damage to the body. In fact, much of the damage in autoimmune disease can be linked to free radical damage to cell membranes and tissues. Studies have shown that oxidative stress and low antioxidant activity occur in autoimmune disease. 

Foods Highest in Antioxidants

  • Goji berries
  • Wild blueberries
  • Artichoke
  • Elderberries
  • Cranberries
  • Blackberries
  • Cilantro

Focusing on nutrient rich foods that are high quality and organic reduces the toxic load on your body and fills the nutritional gaps needed to lower inflammation and support your health.