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Functional Medicine for Autoimmune Disease

Autoimmune disease is on the rise. However, many people suffer years without a diagnosis and remain dissatisfied with the conventional standard of care. In this article, we’ll review our approach to functional medicine for autoimmune disease to treat the root cause, reduce or eliminate your symptoms, and promote true healing in the body.

What is Autoimmunity?

An autoimmune disease occurs when the immune system creates antibodies to mistakenly attack the body’s own tissues. There are roughly 80 autoimmune conditions that affect people worldwide. Women are the most commonly afflicted by these conditions, however, gender ratios differ among specific diseases. For example, women are up to ten times more likely to suffer from Hashimoto’s thyroid disease compared to men (1). Most autoimmune diseases attack one type of tissue, gland, or organ, but symptoms can be widespread, specific, or a general sense of fatigue. Individuals with one autoimmune condition are more likely to eventually develop a secondary autoimmune condition as well. 

A few of the most common autoimmune diseases in the United States include:
  • Hashimoto’s 
  • Graves’
  • Rheumatoid arthritis
  • Psoriasis
  • Celiac disease
The exact cause of autoimmune disease is unknown, however, some researchers have proposed a theory known as the “autoimmunity triad.” This theory suggests that in order for an autoimmune disease to occur, three things must be present: a genetic predisposition, environmental triggers, and intestinal permeability (i.e. leaky gut). 
autoimmune triad

Conventional Treatment

Like most conditions in conventional medicine, treatment is symptom-centered. For example, treatment of hypothyroidism caused by Hashimoto’s typically includes a thyroid medication known as Synthroid or levothyroxine. While levothyroxine may reduce thyroid antibodies (the hallmark feature of Hashimoto’s), this is not always the case. The presence of thyroid antibodies is used for diagnosing Hashimoto’s in conventional medicine but they are otherwise often ignored. Other autoimmune disorders may be treated by taking medications that suppress the immune system. 

Functional Medicine for Autoimmune Disease

Functional medicine is an individualized and science-based approach to treating health conditions by finding the root cause(s) of your autoimmune condition. A functional medicine doctor will dive deeper to find “the why” behind your symptoms. In fact, some of our members do not even realize they have an autoimmune disease until we order appropriate tests confirming the diagnosis!
A functional medicine assessment for autoimmune disease is much more in-depth than a conventional approach. Our doctors & dietitians spend upwards of one hour with members in each visit to listen to your health history and symptom timeline. This gives you space to tell your full story, explain your symptoms, health goals, concerns, and any treatments you may have already tried. We also have access to and knowledge of a wider range of testing, like stool analysis and food sensitivity testing.

Instead of chasing symptoms and suppressing the immune system, a functional medicine approach to autoimmune disease typically involves:

1) Reducing inflammation
2) Healing the gut 
3) Calming the immune response while supporting the body as a whole. 
Here are a few foundational interventions we may recommend for an individual with an autoimmune disease.

Gut Health

More commonly known as a leaky gut, gut permeability is suggested to play a significant role in the development of autoimmune conditions. Dysbiosis (an imbalance of gut bacteria), inflammation, and infection, all compromise the health of your gut and significantly worsen or cause many symptoms.
Since impaired gut health is one of the main players in the development of autoimmune disease, a functional medicine plan almost always involves assessment, testing, and correction of any gut imbalances.This is why we often recommend a comprehensive stool analysis for members in our functional medicine program. 
A functional stool test will assess your gut bacteria and evaluate for any signs of parasites, yeast overgrowth, inflammation, and more. This highly valuable information gives us actionable data to guide your personalized treatment plan that may involve a short-term elimination diet, lifestyle changes, and appropriate supplements, like those found within our Gut Health Bundle.
gut health supplements

Gut Health Bundle

Our 3 most popular gut health supplements bundled together for a 10% savings.

Correcting Nutrient Deficiencies

Certain vitamins and minerals may be associated with the development of autoimmune disease. For example, vitamin D regulates genes involved with inflammation and immune response. Vitamin D deficiency may increase the risk of developing certain autoimmune diseases, like Graves’, psoriasis, Crohn’s disease, ulcerative colitis, and more (2). Alternatively, supplementing with vitamin D may reduce the incidence of autoimmune disease by 22 percent, according to one study (3). Because of its supportive role in supporting immune function, we include a vitamin D blood test for all of our members. Our Vitamin D supplement offers 5,000 units of vitamin D with added vitamin K2 to direct  these nutrients into the bones for optimal use. Other nutrients we may test for individuals with an autoimmune condition include omega-3, magnesium, and zinc.


Your overall diet—as in the foods you eat—is a powerful tool in treating your autoimmune disease. An anti-inflammatory diet is particularly helpful in soothing the immune system, supporting the body with essential nutrients, and supporting gut health. While some people may need a temporary elimination diet to identify and/or remove food sensitivities (gluten being a common one in autoimmune disease), we help members make realistic and sustainable diet changes without unnecessary restriction. Our Root dietitians will collaborate with you to help implement these changes in a way that fits your lifestyle.
Vitamin D3 K2

Vitamin D3 K2

The right dose & form in an easy to swallow capsule
Root Omega 3

Omega 3

Fish oil that goes down easy and boosts Omega-3 levels

Optimizing Your Environment

Do you spend most of your days in a stressful and sedentary environment? Are your meals usually eaten at your desk or on the go? While some of these factors are not necessarily modifiable (i.e. where you work), your lifestyle is a crucial component to a functional medicine treatment for autoimmune disease. We may recommend various interventions to optimize your environment like stress management techniques, vagus nerve activation, and stretching or movement breaks. Additionally, we may suggest cleaner swaps to reduce environmental exposures like using glass or stainless steel instead of plastic and evaluating your cleaning and personal care products. While all of this may sound overwhelming, our Root doctors and dietitians help our members make practical changes that make the most impact.

Key Takeaways

A functional medicine plan for autoimmune disease is a collaborative approach that treats the root cause of your symptoms by using in-depth assessments, personalized testing, and interventions to reduce inflammation through improving gut health, using food as medicine, and optimizing your lifestyle.

Get to the Root at Home 

Curious about where you should start your functional medicine journey? 

Take our Get to the Root Quiz so you can start working towards reversing disease and optimizing your health at the Root cause.
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