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Natural Remedies for Autoimmune Disease

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Like a personal bodyguard, the immune system provides round-the-clock protection. An elaborate network of organs, cells, and proteins supports the immune system as it neutralizes harmful substances and fights infections. We rarely stop to marvel at this near-perfect defense mechanism when it runs like a well-oiled machine. But even the immune system isn’t infallible. When it cannot differentiate between the body’s cells and external threats (bacteria and viruses), the immune system targets its own cells.

Why the Body Attacks Itself

Replicated viruses form circle around hand

Antigens are foreign substances in bacteria, viruses, toxins, cancer cells, and other harmful agents. When the immune system detects dangerous antigens, it produces antibodies to identify and destroy them. Sometimes, this response inadvertently targets healthy cells and tissues, leading to the development of autoimmune diseases.

“The field of immunology is relatively young, and there is so much we don’t know yet about our incredibly intricate immune system,” explains Amy Bader, ND, assistant professor and attending physician at the National University of Natural Medicine in Portland, Oregon. “This makes it difficult to fully understand the causes of these conditions.”

Autoimmune disorders trigger various symptoms, such as joint pain, fatigue, rash, and muscle aches.1Autoimmune Diseases. NIH National Library of Medicine. Medline Plus. October 15, 2021. Symptoms can come and go, but when they’re active, it’s known as a “flare.” Certain factors or events may lead to flare-ups.

“Some triggers are infectious in nature, while others are environmental,” says Dr. Bader. “I have also seen emotional stress and trauma contribute.”

Common Types of Autoimmune Disease

Autoimmune diseases can wreak havoc on normal body processes, destroying tissues, altering organ function, and causing abnormal organ growth.

More than 100 autoimmune disorders exist, and many occur in clusters. Some of the most common autoimmune diseases target one or more systems in the body:

  • Type 1 diabetes targets the pancreas.
  • Rheumatoid arthritis attacks the joints.
  • Inflammatory bowel disease (Crohn’s disease and ulcerative colitis) affects the gastrointestinal tract.
  • Systemic lupus erythematosus affects the brain, joints, skin, lungs, kidneys, and blood vessels.
  • Multiple sclerosis damages nerves in the brain and spinal cord.
  • Graves’ disease triggers overproduction of thyroid hormones.
  • Hashimoto’s disease targets the thyroid.
  • Alopecia areata attacks hair follicles.
  • Psoriasis affects the skin.
  • Psoriatic arthritis strikes skin and joints.
  • Myasthenia gravis weakens muscles.
  • Sjögren’s syndrome affects the entire body.
  • Ankylosing spondylitis fuses bones in the spine.

Celiac disease is an autoimmune condition that causes gluten intolerance. If people with celiac disease consume gluten, their immune system damages the small intestine’s lining and prevents proper absorption of nutrients.2Celiac Disease. National Institute of Diabetes and Digestive and Kidney Diseases. Accessed October 26, 2023.

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Autoimmunity May Be Rising

Seated woman with inflammation places hand on lower back

Autoimmune disease affects more than 50 million people in the United States,3What Is Autoimmunity? Autoimmune Association. Accessed February 23, 2024. 80% of which are women.4Angum F, Khan T, Kaler J, Siddiqui L, Hussain A. The prevalence of autoimmune disorders in women: a narrative review. Cureus. 2020;12(5):e8094. Prevalence of autoimmune disease is on the rise worldwide.5Miller FW. The increasing prevalence of autoimmunity and autoimmune diseases: an urgent call to action for improved understanding, diagnosis, treatment, and prevention. Curr Opin Allergy Clin Immunol. 2023;80. 

Autoimmune disorders can be debilitating, but there is hope for the millions of people who suffer from chronic inflammation, pain, and fatigue. The National Institute of Allergy and Infectious Diseases is supporting more research on autoimmune prevention and treatment by prioritizing clinical trials.6Autoimmune Diseases. National Institute of Allergy and Infectious Diseases. October 6, 2022.

Risk Factors for Autoimmune Diseases

Why immune cells attack is not fully understood. However, scientists believe environmental and genetic factors are at play.7Pisetsky DS. Pathogenesis of autoimmune disease. Nat. Rev. Nephrol. 2023;19:509-524. 30% of autoimmune diseases have a genetic component, while 70% may be due to environmental factors such as toxic chemical exposure, diet, and pathogens.8Vojdani A, Pollard KM, Campbell AW. Environmental triggers and autoimmunity. Autoimmune Dis. 2014;2014:798029.

When genetics contribute to an autoimmune condition, microorganisms (such as bacteria or viruses) or drugs (like those used in chemotherapy) may confuse the immune system, causing it to misfire.9Pisetsky DS. Pathogenesis of autoimmune disease. Nat. Rev. Nephrol. 2023;19:509-524.

Environmental triggers can alter the gut microbiota, leading to increased permeability. Large molecules more easily pass through the intestinal lining, sparking an immune reaction and eventually leading to autoimmunity.10Vojdani A, Pollard KM, Campbell AW. Environmental triggers and autoimmunity. Autoimmune Dis. 2014;2014:798029.

Emotional and Psychological Contributors

Life stressors, conditions such as post-traumatic stress disorder, and emotional trauma all heighten autoimmune risk.11Song H, Fang F, Tomasson G, et al. Association of stress-related disorders with subsequent autoimmune disease. JAMA. 2018;319(23). Scientists believe stress-related hormones affect the immune system by releasing harmful proinflammatory cytokines. Psychological stress can cause dysfunction in the intestinal barrier and digestive tract, increasing systemic inflammation.12Ilchmann-Diounou H, Menard S. Psychological stress, intestinal barrier dysfunctions, and autoimmune disorders: an overview. Front. immunol. 2020;11. 

Inflammation’s Role

Inflammation is a core response of immunodeficiency.13Storrs C. Inflammation: a driving force of autoimmune disease. Global Autoimmune Institute. September 6, 2022. Many conventional treatments for autoimmune conditions work by suppressing immune function, which tempers uncontrolled inflammation.14Jung SM, Kim WU. Targeted immunotherapy for autoimmune disease. Immune Netw. 2022;22(1):e9.

Treating autoimmune disease is nonetheless a complicated process. “This is exactly why a holistic treatment plan is very important,” notes Dr. Bader. “Except for genetics, which cannot be changed, many [contributing] factors can be addressed with naturopathic medicine.”

Natural Support for Autoimmune Disease Symptoms

Mediterranean diet foods displayed in bowl and on cutting board

While autoimmune symptoms greatly vary by person, disorder, and affected organ or tissue, dietary changes are one way to uncover root triggers and possibly stem disease progression.

“When treating autoimmune conditions, it is very important to reduce the burden of inflammation as much as possible, beginning with diet,” says Dr. Bader. “Food can be a big source of inflammation, and it is also something we can control to some degree.”

Dr. Bader starts with an autoimmune protocol (AIP) diet of nutrient-dense fruits and vegetables. Gluten is a no-go for AIP, as are products that may cause inflammation—dairy, refined sugar, fried foods, highly processed foods, trans fats, chemicals, and additives. AIP is similar to Paleo, only stricter, with elimination and reintroduction phases. Research suggests the AIP diet can reduce inflammation and, by avoiding specific triggers, positively affect the gut microbiome.15Konijeti 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.

The Mediterranean diet also mitigates inflammation and may help reduce pain and disease severity, improving quality of life for people with autoimmune disorders.16Tsigalou C, Konstantinidis T, Paraschaki A, Stavropoulou E, Voidarou C, Bezirtzoglou E. Mediterranean diet as a tool to combat inflammation and chronic diseases. An overview. Biomedicines. 2020;8(7):201.

Dr. Bader notes a holistic approach is vital when treating autoimmune disease. “Beyond diet, I also address environmental or infectious triggers,” she says. “I want to optimize health in [every] way possible for my patients with autoimmune conditions. This includes everything from enhancing the gut microbiome to managing stress.”

Correcting nutritional imbalances and incorporating anti-inflammatory supplements such as omega-3 fatty acids from fish oil, vitamins C and D, and curcumin may also help. Natural remedies like prebiotics and probiotics can strengthen and heal the gut lining.


This article is provided by

The Institute for Natural Medicine, a non-profit 501(c)(3) organization. INM’s mission is to transform health care in the United States by increasing public awareness of natural medicine and access to naturopathic doctors. Naturopathic medicine, with its person-centered principles and practices, has the potential to reverse the tide of chronic illness overwhelming healthcare systems and to empower people to achieve and maintain optimal lifelong health. INM strives to fulfil this mission through the following initiatives:

  • Education – Reveal the unique benefits and outcomes of evidence-based natural medicine
  • Access – Connect patients to licensed naturopathic doctors
  • Research – Expand quality research on this complex and comprehensive system of medicine

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