5 Root Causes of Autoimmune Disease and How to Start Healing
ESTIMATED READ TIME: 4–5 MINUTESIf you've been diagnosed with an autoimmune condition, you've probably been told that your immune system has "turned against itself." While there's some truth to that, I don't believe that explanation goes far enough. More importantly, it leaves many people feeling powerless, as if there's nothing they can do beyond managing symptoms.
After decades of working with people battling Crohn's disease, rheumatoid arthritis, Hashimoto's thyroiditis, psoriasis, lupus, multiple sclerosis, and dozens of other autoimmune conditions, I've become convinced of something important: the immune system is usually responding to something. It isn't attacking the body for no reason.
In many cases, there's an underlying trigger keeping the immune system in a constant state of alarm.
Yes, genetics can increase your susceptibility. But genes are rarely the whole story. What matters even more is epigenetics—the environment your genes are exposed to every day.
Your food, your home, your stress, your relationships, your toxic burden, your nutrient status, and your lifestyle can all influence whether certain genes stay quiet or become activated.
Research suggests genetics account for only a portion of autoimmune disease risk, while environmental and lifestyle factors, as well as specific behaviors, determine who ultimately develops disease.
When I was battling severe Crohn's disease, I learned firsthand that healing meant looking beyond symptoms to identify what was fueling inflammation in the first place.
Here are five root causes I encourage people to investigate for themselves.
1. Toxic Burden
Our bodies were designed to detoxify, but today, we're exposed to more toxins than previous generations ever imagined.
Heavy metals, pesticides, herbicides, plastics, industrial chemicals, solvents, polluted air, contaminated water, and thousands of synthetic compounds all place extra stress on our immune systems.
Research increasingly suggests these environmental exposures can contribute to the development of autoimmune diseases by disrupting the gut barrier, altering the microbiome (where the majority of the immune system is found), increasing oxidative stress, and interfering with normal inflammatory responses.
For instance, glyphosate, one of the world's most widely used herbicides, has been linked in certain studies to dysbiosis (imbalance of gut microbes) and a weakened intestinal barrier, which is why some scientists now believe environmental chemicals may contribute to the "leaky gut" often seen in autoimmune disease.
I've also heard powerful personal stories. One example is my friend Stacy Case, who has shared her journey publicly on a recent podcast episode of mine and believes years of exposure to mercury-containing dental fillings contributed to the development of her multiple sclerosis. While every case is different, heavy metal exposure is an area worth discussing with a knowledgeable practitioner, especially when other risk factors are present.
I also encourage people to think beyond obvious toxins and consider commonly used paints, stains, adhesives, furniture, carpeting, fragrances, cleaning products, plastics, and even personal care products they're exposed to every day.
These might seem like "safe" products, but the cumulative effects of constant exposure may not be.
2. Hidden Infections
One of the biggest lessons I've learned is that sometimes the immune system isn't confused; it's actually responding to an ongoing threat and therefore doing its job.
Hidden infections—including certain viruses, bacteria, parasites, and fungal overgrowth—can keep the immune system activated even after an initial illness appears to be over.
Candida overgrowth is one example I frequently see in people who have taken repeated courses of antibiotics or have significant digestive dysfunction. An unhealthy balance of yeast can damage the intestinal lining, alter the microbiome, and contribute to chronic inflammation.
Parasites may also be overlooked, particularly after international travel or contaminated food and water exposure.
Researchers have also identified links between several viral infections and autoimmune diseases. Epstein-Barr virus (EBV), for example, has been associated with an increased risk of multiple sclerosis. In one landmark study involving more than 10 million U.S. military personnel over 20 years, EBV infection increased the risk of developing multiple sclerosis by approximately 32-fold.
That doesn't mean every infection causes autoimmune disease, but it does mean that persistent immune triggers deserve our attention.
3. A Damaged Gut
If you've followed my work for long, you know I believe healing often begins in the digestive system.
Nearly 70% of the immune system resides in or around the gut. When the intestinal lining becomes damaged (a condition commonly called ‘leaky gut’), larger food particles, toxins, and microbial compounds may pass into the bloodstream and provoke an immune response.
Studies have found increased intestinal permeability (‘leaky gut’) in numerous autoimmune diseases including Crohn's disease, celiac disease, type 1 diabetes, rheumatoid arthritis, and Hashimoto's thyroiditis.
This was certainly true in my own life. My digestive system had become so inflamed that my immune system seemed to be on constant high alert. Restoring gut health became one of the biggest turning points in my recovery.
That's why I encourage people to focus on rebuilding the gut with nutrient-dense whole foods, fermented foods when appropriate, collagen-rich bone broth, quality probiotics, and by removing inflammatory triggers whenever possible.
4. Vitamin D Deficiency and Lack of Sunlight
One of God's greatest gifts is also one of the most overlooked: sunshine.
Specifically, UVB rays allow our skin to produce vitamin D, a nutrient that acts more like a hormone than a vitamin and that helps to regulate immune function.
Vitamin D helps regulate T cells, calm excessive immune activation, and support immune tolerance, which is the ability of the immune system to distinguish between harmful invaders and healthy tissue.
Study after study has found that people living with autoimmune diseases are more likely to have low vitamin D levels.
A large review found vitamin D deficiency was associated with multiple autoimmune conditions, including multiple sclerosis, rheumatoid arthritis, inflammatory bowel disease, systemic lupus erythematosus, and autoimmune thyroid disease.
Whenever possible, I encourage safe sun exposure (about 20 minutes, several days per week), especially around midday when UVB rays are available. Depending on where you live, supplementation can also be appropriate, ideally after discussing your levels with your provider.
5. Emotional Trauma and Chronic Stress
You might not suspect that trauma has anything to do with autoimmune diseases, yet I've seen this pattern repeatedly over the years.
Someone experiences a devastating divorce, the death of a loved one, childhood abuse, sexual trauma, financial collapse, or even profound loneliness—and months later, or sometimes years later, they begin experiencing autoimmune symptoms.
Studies now validate that those diagnosed with stress-related disorders, often linked to physical or emotional trauma, have significantly higher rates of autoimmune disease than those without these conditions.
Researchers believe prolonged activation of stress hormones can disrupt normal immune regulation, increase inflammation, alter the microbiome, impair sleep, and weaken the body's resilience. I've especially seen this pattern in women carrying years of unresolved emotional pain.
Trauma and stress don't automatically cause autoimmune reactions, but deep emotional wounds need healing just as much as physical ones. Prayer, counseling, forgiveness, community, time in nature, healthy relationships, and finding purpose can be helpful here.
Healing From an Autoimmune Disease Means Looking Deeper
If you're living with an autoimmune disease, I want to encourage you not to lose hope.
Your diagnosis is not your identity. Instead of only asking, "What medication do I need?" you can ask:
What is my immune system responding to?
What toxic exposures can I reduce?
Is my gut healthy?
Am I carrying hidden infections?
Do I spend enough time in the sunshine?
Is there emotional pain I still need to heal from?
When I overcame Crohn's disease, it required removing what was harming my body while restoring what I was made to receive: nourishing food, clean water, fresh air, sunshine, movement, meaningful relationships, rest, gratitude, and faith.
Your body has an incredible capacity to heal when you remove obstacles and provide the building blocks it needs. And sometimes the first step isn't fighting back against your immune system but understanding why it's struggling in the first place.
References:
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https://link.springer.com/article/10.1007/s11154-026-10026-9
https://pmc.ncbi.nlm.nih.gov/articles/PMC6759203/
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