Functional medicine begins with a simple principle. Each person is biochemically unique, which means one treatment cannot work for everyone. Conventional medicine often treats symptoms tied to a specific organ. Functional medicine takes a broader view and looks deeper to identify the root cause of autoimmune disease.
Before I became a physician, functional medicine practitioner, and two-time New York Times bestselling author, I experienced my own autoimmune diagnosis. I understand how frustrating it can feel when symptoms appear, and clear answers are difficult to find.
Hear my story on this episode of Take Back Your Health™.
Table of Contents:
- What Is Autoimmune Disease?
- The Immune System: A Root Cause of Autoimmune Disease
- Autoimmune Disease and Conventional Medicine
- Supporting the Immune System Instead of Suppressing It
- 5 Underlying Causes of Autoimmunity
- The Myers Way® Approach to Addressing Autoimmunity
- The Final Word on the Causes of Autoimmunity
- Autoimmune Disease FAQs
Many patients are told that autoimmune disease is genetic and permanent. They are often prescribed medications designed to suppress the immune system. These medications may reduce symptoms for some individuals. They rarely address what causes autoimmune disease in the first place.
Genetics certainly influences risk. However, your environment often determines whether those genes become activated. Research continues to show that autoimmunity often develops when the immune system becomes overwhelmed by environmental triggers.(1)
When these triggers persist, the immune system may begin producing autoantibodies that mistakenly attack healthy tissues. The encouraging news is that identifying and addressing these triggers may support immune balance and help calm autoimmune activity. To understand how this happens, it helps to first understand what autoimmune disease is and how the immune system functions.
What Is Autoimmune Disease?
Autoimmune disease occurs when the immune system mistakenly attacks the body’s own tissues.
Your immune system protects you from harmful invaders such as bacteria, viruses, and toxins. Under normal circumstances, the immune system distinguishes between foreign threats and healthy cells. In autoimmune disease, this recognition system breaks down. The immune system begins targeting normal cells as though they were dangerous invaders.(2)
More than 80 autoimmune diseases have been identified. These conditions affect different organs and tissues throughout the body.
Common autoimmune diseases include:
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Rheumatoid arthritis
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Systemic lupus erythematosus
- Hashimoto’s thyroiditis
- Graves’ disease
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Multiple sclerosis
- Type 1 diabetes
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Psoriasis
- Celiac disease
Learn more about autoimmune disease with Dr. Sara Gottfried on this episode of Take Back Your Health™ podcast
The Immune System: A Root Cause of Autoimmune Disease
Every autoimmune condition begins with immune system dysregulation. Your immune system contains two primary defense systems that work together to protect your body.
Innate Immune System
The innate immune system provides immediate protection against potential threats. It includes your skin, mucous membranes, immune cells, and protective proteins that serve as your first line of defense. This system reacts quickly whenever the body detects bacteria, viruses, or physical injury.
Adaptive Immune System
The adaptive immune system provides a more targeted response. It consists of specialized immune cells, including T cells, B cells, and antibodies. This system learns from previous exposures and remembers specific pathogens so it can respond more efficiently in the future.(3)
In autoimmune diseases, the adaptive immune system may begin producing autoantibodies that mistakenly target healthy tissues rather than harmful invaders. Once this process begins, inflammation and tissue damage can develop.
The next question becomes clear: what causes the immune system to misfire in the first place?
Autoimmune Disease and Conventional Medicine
In conventional medicine, autoimmune diseases are typically treated based on the organ involved.
Examples include:
- Rheumatologists for joint diseases
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Endocrinologists for thyroid conditions
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Gastroenterologists for digestive disorders
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Dermatologists for skin conditions
Each specialist focuses on the affected organ system.
Many individuals eventually develop multiple autoimmune diseases, a pattern known as polyautoimmunity.(4) This often leads to visits with several specialists and the use of multiple medications.
These medications may help manage symptoms by suppressing immune activity or reducing inflammation. They do not address the underlying triggers that caused immune dysfunction.
Functional medicine takes a different approach. Instead of asking which medication to prescribe, we ask an important question. Why did the immune system lose balance in the first place?
Supporting the Immune System Instead of Suppressing It
Immune suppression can reduce inflammation and help control symptoms. It does not restore immune health. Functional medicine focuses on supporting immune balance while addressing the triggers that drive chronic inflammation.
Several factors frequently contribute to ongoing immune activation:
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Gut barrier damage
- Food sensitivities
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Environmental toxins
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Chronic infections
- Long-term stress
When these triggers remain present, the immune system stays on high alert. Over time, this persistent immune activation can increase the risk of autoimmune disease. Understanding these triggers provides a roadmap for healing.
5 Underlying Causes of Autoimmunity
Autoimmune disease usually develops from multiple triggers that disrupt immune balance. The most common causes include gut dysfunction, inflammatory foods, toxins, infections, and chronic stress.
1. Leaky Gut
A weakened gut lining allows food particles, bacteria, and toxins into the bloodstream, triggering immune activation. Nutrient-dense, AIP-friendly foods such as bone broth, leafy greens, fermented vegetables, and wild-caught fish support gut health and help calm autoimmune activity.
2. Gluten
Gluten can increase intestinal permeability and promote immune confusion through molecular mimicry. Removing gluten is often essential for reducing inflammation and supporting immune balance.
3. Environmental Toxins
Heavy metals, pesticides, mold toxins, and plastics can overwhelm the immune system and drive inflammation. Reducing exposure by eating organic foods, drinking filtered water, and using non-toxic products can protect immune health.
4. Chronic Infections
Persistent or reactivated infections, including Epstein-Barr virus, herpes simplex virus, and E. coli, may trigger chronic immune activation and contribute to autoimmunity. Supporting immune resilience is key to reducing their impact.
5. Chronic Stress
Ongoing stress keeps the immune system on high alert, increasing inflammation and the risk of autoimmune disease. Daily practices such as breathing exercises, meditation, gentle movement, and time outdoors can restore immune balance.
The Myers Way® Approach to Addressing Autoimmunity
The Myers Way® is a proven approach to chronic illness that gets to the root of symptoms. This lifestyle rests on four pillars to reach the root cause of autoimmune disease, so you can reverse your condition and take back your health!
Pillar I: Heal Your Gut
You begin by healing the gut. In functional medicine, we use the proven 4R approach:
- Remove the bad – Get rid of factors that negatively impact the environment of your gastrointestinal tract, such as toxins and inflammatory foods, as well as intestinal infections like SIBO and yeast overgrowth.
- Restore what’s missing — Add Gut Restore with Betaine and HCL and digestive enzymes to your daily regimen to help support digestion and nutrient absorption.
- Reinoculate with healthy bacteria — Restore beneficial bacteria with a probiotic supplement to re-establish a healthy balance of bacteria to heal your gut.
- Repair the gut — Provide the necessary nutrients to help the gut repair itself. The Leaky Gut Support Protocol supports your immune system and gut lining. It now comes in three different flavors to satisfy different taste buds. Adding collagen protein or drinking bone broth will also help to heal your gut.
Pillar II: Get Rid of Gluten, Grains, and Legumes
Once you’ve healed your gut, it’s time to make diet changes. Start by eliminating foods such as gluten, grains, and legumes that can damage your intestinal tract and cause inflammation. I also recommend avoiding nightshades, which include peppers, tomatoes, and potatoes. These plants are very high in lectins that damage the gut lining, quickly enter the bloodstream, and do not break down in cooking.
Pillar III: Tame the Toxins
Many patients notice improvement after addressing the first two pillars. If you do not see progress, your toxin burden may be overflowing. We are exposed to thousands of toxins every day. They are in the water you drink, the air you breathe, the food you eat, and the cookware, cleaning products, and cosmetics you use.
Unfortunately, we cannot avoid toxins altogether. As such, the solution is to reduce your body’s toxic burden by:
- Buying clean skincare and body products
- Cleaning your air by getting a HEPA filter for your home. I use AIRDoctor® air filters in my home.
- Buy clean food and eat organic whenever possible. It can be expensive, so buy free-range chicken, grass-fed beef, and wild-caught seafood at the very least.
- Clean your water by installing water filters on your shower taps and sinks. I have a complete filtration system from Aquasana.
Pillar IV: Heal Your Infections and Relieve Your Stress
If your symptoms haven’t cleared up after addressing the first three pillars, it’s time to dig deeper. The fourth pillar of The Myers Way® focuses on healing your infections and relieving your stress.
To relieve stress, I suggest adopting daily stress-relieving strategies and adding Adrenal Support. Adrenal Support promotes a more balanced physical and emotional stress response using a cutting-edge blend of adaptogenic herbs.
For total support, The Autoimmune Solution™ Protocol combines four of the most important nutritional supplements for anyone concerned with autoimmunity. Your immune system is a complex puzzle influenced by multiple aspects of health. The integrity of your gut barrier, oxidative damage done by free radicals, inflammation, toxic load, detoxification, and much more all play a role in how your immune system functions.
The Final Word on the Causes of Autoimmunity
Receiving an autoimmune diagnosis can feel overwhelming. I want you to know there is hope!
Autoimmune diseases often share common root causes, including gut dysfunction, toxins, infections, food sensitivities, and chronic stress. When these triggers are addressed, the immune system often regains balance. This principle forms the foundation of The Myers Way®.
I have seen thousands of patients improve their health by identifying and addressing the root causes of autoimmune disease. With the right support such as following The Autoimmune Solution™ Protocol, your body has a remarkable ability to restore balance and move toward healing.
Autoimmune Disease FAQs
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What causes autoimmune disease?
Autoimmune disease occurs when the immune system mistakenly attacks healthy cells and tissues. While genetics can influence risk, many experts believe environmental triggers such as gut health issues, food sensitivities, infections, toxins, and chronic stress play a significant role in the development of autoimmunity. -
What are the most common root causes of autoimmune disease?
Common root causes of autoimmune disease include intestinal permeability, often called leaky gut, gluten sensitivity, environmental toxins, chronic infections, and long-term stress. These factors can disrupt immune system balance and trigger inflammation that contributes to autoimmune conditions. -
Can autoimmune disease be linked to gut health?
Yes. The gut plays a major role in immune system function because a large portion of immune cells reside in the digestive tract. When the intestinal barrier becomes compromised, substances can enter the bloodstream and trigger immune reactions that may contribute to autoimmune disease. -
Can supplements help support autoimmune health?
Certain supplements may help support immune balance and gut health, which are important factors in autoimmune disease. Nutrients that support gut integrity, probiotics for microbiome balance, and antioxidants such as glutathione may help support the body’s natural immune response. Many functional medicine protocols also include targeted supplements designed to support gut repair, detoxification, and immune system health. -
Can you have more than one autoimmune disease at the same time?
Yes. It is possible to have more than one autoimmune disease, a situation sometimes referred to as polyautoimmunity. Because autoimmune conditions often share similar underlying triggers such as immune system imbalance, gut dysfunction, infections, and environmental factors, some individuals may develop multiple autoimmune conditions over time. Addressing the underlying causes of immune dysfunction may help support overall immune health.
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