This article is part of a special report on Thyroid Disorders. To see the other articles in this series, click here.

In the first article in this series, I showed that hypothyroidism is an autoimmune disease in 90% of cases. In this article we’re going to discuss the connection between autoimmune thyroid disease (AITD) and gluten intolerance.

Several studies show a strong link between AITD (both Hashimoto’s and Graves’) and gluten intolerance. [1, 2, 3, 4, 5] The link is so well-established that researchers suggest all people with AITD be screened for gluten intolerance, and vice versa.

What explains the connection? It’s a case of mistaken identity.

The molecular structure of gliadin, the protein portion of gluten, closely resembles that of the thyroid gland. When gliadin breaches the protective barrier of the gut, and enters the bloodstream, the immune system tags it for destruction.

These antibodies to gliadin also cause the body to attack thyroid tissue. This means if you have AITD and you eat foods containing gluten, your immune system will attack your thyroid.

Even worse, the immune response to gluten can last up to 6 months each time you eat it. This explains why it is critical to eliminate gluten completely from your diet if you have AITD. There’s no “80/20” rule when it comes to gluten. Being “mostly” gluten-free isn’t going to cut it. If you’re gluten intolerant, you have to be 100% gluten-free to prevent immune destruction of your thyroid.

So how do you find out if you’re gluten intolerant? Unfortunately, standard lab tests aren’t very accurate. They test for antibodies to gluten in the bloodstream. But antibodies in the blood will only be found in cases where the gut has become so permeable that gluten can pass through. This is a relatively advanced stage of disease. Blood tests will miss the many milder cases of gluten intolerance that haven’t yet progressed to that stage.

Stool analysis is far more sensitive, because it detects antibodies produced in the digestive tract that aren’t yet escaping into the bloodstream. Using this method at Entero Lab, Dr. Kenneth Fine, a pioneer in the field, has found that up to 35% of Americans are gluten intolerant.

In addition to the stool analysis, Dr. Fine’s lab uses a cheek swab to test for the genes connected with gluten intolerance and celiac disease. People with HLA DQ genes are more likely than the general population to have autoimmune disease, celiac disease and gluten intolerance. Dr. Fine’s research shows that more than 80% of Americans have one of these gene types.

When I first read Dr. Fine’s research, I was astounded by the implications. It suggests that 1 in 3 Americans are gluten intolerant, and that 8 in 10 are genetically predisposed to gluten intolerance. This is nothing short of a public health catastrophe in a nation where the #1 source of calories is refined flour. But while most are at least aware of the dangers of sugar, trans-fat and other unhealthy foods, fewer than 1 in 8 people with celiac disease are aware of their condition. I would guess that an even lower proportion of people are aware they are gluten intolerant.

One reason gluten intolerance goes undetected in so many cases is that both doctors and patients mistakenly believe it only causes digestive problems. But gluten intolerance can also present with inflammation in the joints, skin, respiratory tract and brain – without any obvious gut symptoms.

As much improved as Dr. Fine’s methods are, they aren’t perfect. In some patients with autoimmune disease, their immune system is so worn out they can no longer produce many antibodies.

Hashmioto’s, the most common autoimmune thyroid condition, is primarily a Th1 dominant condition. I’ll explain what this means in further detail in a future article. For now, what you need to understand is that in Th1-dominant conditions, the Th2 system is suppressed. The Th2 system is the part of the immune system responsible for producing antibodies. When the Th2 system is severely depressed, the body’s ability to produce antibodies is impaired. The levels may be so low that they won’t show up on a test. So, even if you have gluten intolerance, your test for gluten antibodies may be falsely negative if you have Th1-dominant Hashimoto’s.

This is why I recommend that you avoid gluten if you have AITD, regardless of whether tests show an active antibody response. This is especially true if you have one of the genes (HLA DQ1,2, or 3) that predisposes you to developing gluten intolerance. In my opinion continuing to eat gluten when you have a confirmed autoimmune condition simply isn’t worth risking the immune destruction it could cause.

In fact, the more I learn about gluten and its effects on the body, the more I think we’d all probably be better off not eating it. Mark Sisson has written extensively about the dangers of gluten and gluten-containing grains, so head over there and have a look if this is new to you.

The short version: foods that contain gluten (both whole grains and flours) contain substances that inhibit nutrient absorption, damage our intestinal lining, and – as I’ve described in this article – activate a potentially destructive autoimmune response. What’s more, there are no nutrients in gluten-containing foods that you can’t get more easily and efficiently from foods that don’t contain gluten.

The good news is that if you have AITD and are gluten intolerant, removing gluten completely from your diet will dramatically improve your health. It’s not easy, but it’s worth it.