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Diet’s Role in Autoimmunity

By Anne Danahy, MS, RDN

If you feel like you’re seeing more patients lately with autoimmune diseases, you’re probably right. Autoimmunity is rising in the United States, especially among males, non-Hispanic whites, adults aged 50 and older, and adolescents.1

What follows is a discussion on the definition of autoimmunity and an evaluation of the current research on the possible risk factors that may lead to autoimmune disease and how diet may play a role in prevention and management.

What Is Autoimmunity?
In autoimmunity, the immune system mistakenly attacks healthy cells. Although everyone has some degree of autoimmunity, it can progress to an autoimmune disease in some people. According to the American Autoimmune Related Disease Association, there are at least 100 autoimmune diseases that affect nearly every organ or system in the body.2 

Autoimmunity is commonly identified by the presence of antinuclear antibodies (ANA). A June 2020 study in Arthritis & Rheumatology found the prevalence of ANA increased from 11% to 15.9% between 1998 and 2012 in the United States.1

Although anyone can develop autoimmune disease, it tends to affect twice as many females as males. For example, systemic lupus erythematosus (SLE) and Sjogren’s syndrome affect mainly women. Some common autoimmune diseases (and the organs or tissues most often affected) include the following2,3:

• SLE (can affect any system or organ);
• celiac disease (intestinal villi);
• inflammatory bowel disease (IBD) (gastrointestinal tract);
• Sjögren’s syndrome (fluid-secreting glands);
• psoriasis (skin);
• Hashimoto’s thyroiditis/Grave’s disease (thyroid gland);
• rheumatoid arthritis (RA) (joints);
• systemic sclerosis (skin and collagen-containing organs);
• multiple sclerosis (MS) (central nervous system); and
• type 1 diabetes (pancreatic islet cells).

The Common Thread
Autoimmune diseases are a mystery, but they seem to have some common threads. These include genetics, environmental exposures, and physical or emotional stress from infection, hormonal changes, or a difficult life event. With the right combination, these factors can cause the immune system to misfire and attack healthy cells and tissues.

It’s believed that autoimmune diseases likely have a genetic component, because they often run in families. It’s not uncommon for several members of a family to have different autoimmune diseases.2

Environmental triggers such as certain medications, cigarette smoke, alcohol, and UV radiation play a role in promoting autoimmune diseases. Diet also contributes. Those who eat a diet high in proinflammatory foods, such as refined grains or added sugars, are more at risk.2,4,5

However, for the most part, the exact mechanisms aren’t clear. In some cases, exposure to toxic compounds can alter gene expression. In others, toxins may cause cytokine (proteins that signal immune cells) dysregulation. Certain foods or diet patterns may disrupt the immune functions in the gut microbiome or promote inflammation.4,5

Autoimmune Diseases and the Western Diet
Research shows the Western diet, which is high in calories, fat, salt, sugar, and processed foods, can promote autoimmune disease, and studies point to several different mechanisms by which this is possible.5-7

A Western diet contributes to obesity, metabolic syndrome, and inflammation. Visceral obesity in particular increases the secretion of proinflammatory adipokines. These adipokines promote systemic inflammation, which impacts T-cell function, and may promote autoimmune disease.5 

Diet patterns shape the gut microbiome. A Western diet, high in fat and low in plant foods, promotes dysbiosis, or an unfavorable change in the microbiome. This is significant because the gut microbiota help regulate many aspects of the immune system. Dysbiosis likely plays a role in both the development and progression of autoimmune diseases such as IBD, autoimmune thyroid disease, MS, RA, and celiac disease.6 

High sodium intake is associated with more than double the risk of RA among smokers and greater clinical features of MS. Lab and animal studies suggest this may be because excess sodium activates or upregulates production of T helper cells and may worsen autoimmune disease progression.7

Leaky Gut
Various components of a Western diet, including excess calories, added sugars, saturated fat, animal protein, and alcohol, can lead to increased intestinal permeability, known as leaky gut.6,8 Intestinal permeability enables certain undigested proteins to escape the GI tract and enter the body, causing an immune reaction. In addition to the Western diet, some people are sensitive to proteins in wheat, gluten, cow’s milk, soybeans, corn, and nightshade vegetables. These are thought to worsen intestinal permeability and further contribute to autoimmune diseases.8 However, more research is needed in this area to determine a causal relationship.

Diet as Essential Part of Treatment
To date, there’s no cure for autoimmune diseases, but medication, diet, and lifestyle changes can help manage symptoms.

“Counseling patients with these complex conditions can be confusing because there’s no one evidence-based diet for autoimmune disease,” says Nina Young, MS, RDN, ACE-GFI, a Los Angeles–based dietitian who specializes in autoimmune diseases. “However, identifying and correcting any nutritional deficiencies or inadequacies is always a helpful starting point.”

Some studies suggest vitamin D’s anti-inflammatory properties may play a role.9 “Vitamin D levels often are low with autoimmune diseases,” Young says. “Supplementing as needed and maximizing immune-modulating nutrients such as fiber, probiotics, and omega-3s is beneficial.”

The following diet patterns are sometimes used in autoimmune disease management, and Young agrees there are components of each that all can be helpful:

Mediterranean diet. With a focus on plant foods, fruits, vegetables, legumes, whole grains, healthful fats, and fiber, this diet pattern can support the microbiome and the health of the digestive tract. Studies also show it reduces inflammatory markers in patients with RA and Crohn’s disease.7 

Gluten-free diet. Gluten has been implicated not only in celiac disease, but also in autoimmune thyroid disease. Some studies suggest that even in those without celiac, gluten irritates the digestive tract, promotes dysbiosis, alters intestinal permeability, and is proinflammatory.7 

Paleolithic diet. This trendy diet restricts grains, legumes, dairy, sodium, processed carbohydrates, and refined oils such as corn and soybean oil. It eliminates many components of the Western diet, and thus may promote weight loss, reduce inflammation, and modulate the immune response. However, there are limited studies on its efficacy in autoimmune disease.7 

Autoimmune Protocol Diet (AIP). An extension of the Paleo diet, the AIP diet eliminates nightshade vegetables, eggs, coffee, alcohol, nuts, seeds, and food additives in addition to the foods eliminated in the Paleo diet. The focus is on fresh, nutrient-dense foods, fermented vegetables, high-quality proteins, and bone broth. Research shows the AIP diet may reduce inflammation and rectal bleeding in IBD and improve health-related quality of life measures in autoimmune thyroid disease.10,11 

Young emphasizes that some of these diets are restrictive. “Any diet pattern should be individualized based on patient preferences, disease severity, and motivation to make diet changes,” she says.

Much is still unknown about what causes autoimmune disease and the best ways to manage it. But because diet is one modifiable risk factor, those at risk can benefit from making such changes. RDs should guide patients to get back to the basics: choosing nutrient-dense whole foods, limiting highly processed foods, and aiming for healthy vitamin D levels. These can make a big difference in managing symptoms or preventing autoimmune diseases altogether.

— Anne Danahy, MS, RDN, is the owner of AnneDanahy.com. She provides nutrition communications and content writing services for health and wellness brands. She’s also a freelance writer with Dietitian Pros Premier Nutrition Staffing. Dietitian Pros provides class-leading nutrition staffing services across the United States and recruits RDs to serve in temporary, part-time, or full-time positions. 


1. Dinse GE, Parks CG, Weinberg CR, et al. Increasing prevalence of antinuclear antibodies in the United States. Arthritis Rheumatol. 2020;72(6):1026-1035.

2. American Autoimmune Related Disease Association, Inc website. https://www.aarda.org. Accessed February 25, 2021.

3. Angum F, Khan T, Kaler J, Siddiqui L, Hussain A. The prevalence of autoimmune disorders in women: a narrative review. Cureus. 2020;12(5):e8094.

4. Wang L, Wang FS, Gershwin ME. Human autoimmune diseases: a comprehensive update. J Intern Med. 2015;278(4):369-395.

5. Manzel A, Muller DN, Hafler DA, Erdman SE, Linker RA, Kleinewietfeld M. Role of “Western diet” in inflammatory autoimmune diseases. Curr Allergy Asthma Rep. 2014;14(1):404.

6. Leech B, McEwen B, Sekyere EO. Diet, digestive health, and autoimmunity: the foundations to an autoimmune disease food pyramid—part 1. Altern Complement Ther. 2020;26(3):112-118.

7. Leech B, McEwen B, Sekyere EO. Diet, digestive health, and autoimmunity: the foundations to an autoimmune disease food pyramid—part 2. Altern Complement Ther. 2020;26(4):158-167.

8. Leech B, McIntyre E, Steel A, Sibbritt D. Risk factors associated with intestinal permeability in an adult population: a systematic review. Int J Clin Pract. 2019;73(10):e13385. 

9. Yamamoto E, Jørgensen TN. Immunological effects of vitamin D and their relations to autoimmunity. J Autoimmun. 2019;100:7-16.

10. Konijeti GG, Kim N, Lewis JD, et al. Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflamm Bowel Dis. 2017;23(11):2054-2060.

11. Abbott RD, Sadowski A, Alt AG. Efficacy of the autoimmune protocol diet as part of a multi-disciplinary, supported lifestyle intervention for Hashimoto’s thyroiditis. Cureus. 2019;11(4):e4556.