What Causes Autoimmune Disease?
Q: Autoimmune diseases seem to be so prevalent these days. Why is this? Is there anything we can do? — R. Pierce, Biloxi, MS
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A: What causes auto immune disease? There are between 80 and 100 autoimmune diseases, and only one of them—one of them—has a known, identified trigger.
I’ll let that sink in for a minute. That means we know the cause of only one specific autoimmune disease—celiac, which is triggered by gluten, 100 percent of the time. The rest are something of a mystery.
The list of autoimmune diseases is pretty daunting. Multiple sclerosis, Alzheimer’s disease, diabetes, inflammatory bowel disease (colitis and Crohn’s), ALS (Lou Gehrig’s disease), thyroid disease (Graves and Hashimoto’s), psoriasis, and rheumatoid arthritis are all autoimmune diseases, and that’s just a partial list. What’s more, experts like Tom O’Bryan, author of The Autoimmune Fix, and Amy Myers, MD, author of The Autoimmune Solution, regard autoimmunity on a spectrum, with the fully diagnosed, identifiable “disease” state being just one arbitrary point on that spectrum.
Most of us probably fall somewhere on this spectrum, and have some degree of autoimmunity dysfunction—some less so, some more so. And we should all be paying attention. Autoimmune dysfunction is likely happening well in advance of any noticeable symptoms.
In one fascinating study, Melissa Arbuckle, MD, PhD, looked at the patient history of 130 vets in the VA hospital system, all of whom had been diagnosed with lupus, a systemic autoimmune disease. Those in the service have their blood drawn regularly throughout their tours of duty, so Arbuckle looked back at their records. Every single one of them had markers for no less than seven different antibodies—years before they actually showed symptoms and got a lupus diagnosis.
As O’Bryan puts it, “You can’t argue with antibodies.” Thyroid antibodies, for example, show up in the blood—a sure sign of immune system activity—well in advance of thyroid hormone abnormalities. O’Bryan, Myers, and others who share this view believe that the time to be aware of how your immune system is doing is now—even if you’ve never been diagnosed with an autoimmune disease.
O’Bryan and Myers are practitioners of functional medicine, an approach that sees the body as a functioning whole in which each part affects all the other parts. Functional medicine practitioners understand and investigate all components of a patient’s health, not just his or her identified disease. It’s an approach that’s uniquely suited to autoimmune disease.
Understanding the Immune System and What Causes Auto Immune Diseases
The job of the immune system is to defend against foreign invaders. It’s like having your own personal, built-in Homeland Security system, the only job of which is to keep you safe. This security system consists of all kinds of specialized immune system cells like T-cells, B-cells, and macrophages, all of which are on the alert for something that doesn’t belong in your body or in your bloodstream. When a threat is perceived, instructions are simple: take it out!
When this system is working well, it does indeed keep you safe—or at least safe from illnesses caused by unfriendly microbes. But sometimes, the complex, ever-vigilant immune system makes a mistake. That mistake is the immune system equivalent of an army’s “friendly fire.” Your immune system misidentifies as a “foreigner” something that has a perfect right to be there. It thinks there’s a threat when there isn’t one.
When your immune system attacks the myelin sheath that covers your nerves, it’s called multiple sclerosis. When it attacks the thyroid, it’s Hashimoto’s thyroiditis. When it attacks the glands that produce tears and saliva, it’s Sjogren’s syndrome. And when it attacks cells and tissues throughout the body, affecting anything from the joints to the heart, it might be lupus.
Inflammation and Auto Immune Disease
O’Bryan recalls a metaphor for this that he learned from Jeffrey Bland, PhD, considered the father of functional medicine. Bland likened the inflammatory response in the body to filling a football field with mousetraps laid side by side, each loaded with a ping pong ball. If you then toss an additional ping pong ball on top, bam! Suddenly there are two balls in the air, the one you tossed into the field and the one that popped out of the mousetrap it set off. These balls hit a couple more mousetraps, and eventually all the mousetraps will be set off, making the whole thing sound like a fireworks display on the 4 of July.
That’s how autoimmune diseases often work. Something—a food, a component of food, a toxin, sugar, a chemical, even a stressful life event—triggers inflammation, but then the oxidative stress that goes hand in hand with inflammation increases faster than what your internal antioxidant army can keep up with.
When your immune system is set off by triggers like gluten or toxins, your own tissue could be collateral damage.
Myers believes that there are four key factors triggering the alarming increase in autoimmune disorders: The first is gluten, which is ubiquitous in our diet, and znflammatory for many people. It’s also often found in foods that have other inflammatory components like sugar.
Toxins are the second factor. They’re everywhere and we’re exposed to them in all sorts of combinations. At some point the cumulative effect—what’s called the toxic burden—overwhelms the body’s ability to fight back, weakening immunity even further.
Stress, the third factor, can trigger—and make worse—autoimmune diseases. Myers thinks this plays a significant part in the current autoimmune epidemic.
Finally, there’s leaky gut. The lining of the intestines is, amazingly, only one cell thick. Think of it as a thin layer of cheesecloth, protecting the bloodstream from particles that don’t belong. But sometimes there are tears in the cheesecloth, and the lining of the gut is said to “leak.” This allows bigger, less digested particles called macromolecules to get through the “cheesecloth” and go into the bloodstream. The immune system looks at these molecules and calls out the troops. The cycle of inflammation, leaky gut, and more inflammation continues. That’s why healing the gut is so high on the list of priorities for any functional medicine approach to autoimmunity.
Healthy tip!
An apple a day, along with other antioxidant, anti-inflammatory foods, can help improve symptoms of autoimmune diseases.
Functional Approach to Treating Auto Immune Disease

Any real, effective treatment plan has to include every aspect of life—diet, sleep, stress, and emotions. The organ that’s affected—the place where you actually see and feel the symptoms—is the sole focus of conventional medicine, but it is just the starting point for a functional approach to autoimmune disease.
The functional approach sees the total interconnectivity of everything you do—from eating foods high in natural anti-inflammatories and antioxidants, to taking inflammation-quenching supplements, to getting enough sleep, to having enough joy in your life, to moving your body and strengthening your gut. The functional approach goes way beyond simply “managing” symptoms with harsh pharmaceuticals—it offers a message of hope.
Did you know…
The functional medicine approach addresses the physical and emotional aspects of disease treatment.