Gluten, Leaky Gut, and Autoimmune Thyroid Disease
Thanks to the pioneering work of Dr. Alessio Fasano*, we know that leaky gut is one of the primary triggers for all autoimmune disease, including autoimmune thyroid disease. As you might guess by its name, leaky gut occurs when your gut (specifically your small intestine) becomes permeable, allowing particles to leak from your digestive tract and travel freely through your bloodstream.
Gluten is one of the main causes of leaky gut in people that I see with thyroid issues and autoimmune diseases, and not just among Celiac patients, but in anyone with gluten sensitivity. When anyone, whether they have gluten sensitivity or not, eats a gluten-containing food, the gluten proteins make their way through the stomach and arrive at the small intestine, where the body responds by producing zonulin, a chemical that signals the tight junctions of the intestinal walls to open up, creating temporary permeability. This permeability will heal as the gut cells renew every 48 hours. However, if you have gluten sensitivity and you eat gluten, then this permeability will not heal in that 48 hours and your gut remains leaky. Leaky gut can also be caused or exacerbated by gut infections such as Candida overgrowth or SIBO, medications such as antibiotics, steroids or birth control pills, as well as a high stress lifestyle. New research shows that spraying Glyphosate (Roundup) on the wheat is also a major contributor of leaky gut and gluten sensitivity.
Now that your small intestines are open and permeable this allows toxins, microbes, and partially digested food to leak into your bloodstream, your immune system goes on high alert to neutralize all of these threats. But, because your gut is still leaky, the threats just keep on coming, putting your body in a state of chronic inflammation and putting you on the path to develop an autoimmune disease (including thyroid dysfunction) as your immune system becomes so stressed and confused that it begins attacking your own tissue by mistake. Unfortunately, the gluten that caused your gut to become leaky makes it even more likely that you will develop thyroid dysfunction (autoimmune and non autoimmune), thanks to a phenomenon called molecular mimicry.
*PubMed – Leaky Gut and Autoimmune Disease
Molecular Mimicry, A Case of Mistaken Identity
Every time your body is exposed to a bacteria, virus, or other pathogen, your immune system memorizes its structure, specifically its protein sequence, so that it can recognize it in the future and mount a defense.
However, the immune system’s recognition system isn’t foolproof; as long as a molecule’s structure and protein sequences are similar enough, the immune system can be fooled into attacking look-a-like molecules that are actually your body’s tissue, causing autoimmune disease. Unfortunately for the thyroid, it has a common doppelgänger that puts it at risk for rogue autoimmune attacks. You guessed it – gluten. What’s more, 50% of people with gluten sensitivity experience molecular mimicry with casein (a protein found in dairy). This is known as cross-reactivity, where you react not only to your original trigger, but also to another trigger that resembles the first one.

Thanks to the leaky gut that was originally caused by gluten, every time you eat gluten and dairy, their proteins are able to escape into your bloodstream, where they trigger an attack from your immune system. And, because of the molecular mimicry phenomenon, your thyroid tissues end up in the crosshairs as well.
Interestingly, your immune system’s attack can affect your thyroid in two completely different ways. In the case of autoimmune hypothyroidism (Hashimoto’s disease) your immune system’s attacks decrease thyroid functionality, so your metabolic processes slow down. In autoimmune hyperthyroid (Grave’s disease), the antibodies act like Thyroid Stimulating Hormone, causing your thyroid to overproduce its hormones and sending your metabolism into overdrive.
Even in patients who have non-autoimmune thyroid disease, the molecular mimicry phenomenon still impacts thyroid function, which is why I recommend that all of my patients with thyroid dysfunction remove gluten from their diet, even if they are not autoimmune.