Woman looking at bread

Why Gluten Is a Problem for Autoimmune Disease

If you have Hashimoto's, Graves', lupus, rheumatoid arthritis, or any other autoimmune condition, you have probably heard that diet plays a role in how you feel. In my experience, both as a physician and as someone who has lived with autoimmune disease, there is one food above all others that can derail your progress: gluten.

I know that giving up gluten feels overwhelming at first. However, once you understand what gluten actually does in your body, the decision becomes much clearer. Here are the three reasons I recommend that every one of my patients with autoimmune disease go completely gluten-free.

Diagnosis of autoimmune disease in a diagram

Table of Contents:

  1. Why Gluten Is a Problem for Autoimmune Disease
  2. Gluten Triggers Leaky Gut
  3. Gluten Drives Chronic Inflammation
  4. Gluten Mimics Your Own Tissues
  5. How to Repair the Damage
  6. FAQs

Gluten Triggers Leaky Gut

When you eat gluten, it travels through your stomach and into your small intestine. There, it triggers the release of a protein called zonulin. Zonulin signals the tight junctions of your intestinal wall to open up, creating what is known as intestinal permeability, or leaky gut.(1)

Think of your gut lining as a drawbridge. When everything is functioning optimally, only small, properly digested micronutrients pass through. When gluten releases zonulin, that drawbridge goes up, and larger particles that were never meant to enter your bloodstream slip through. That includes microbes, toxins, and partially digested food particles such as gluten itself.

Research from Dr. Alessio Fasano confirms that leaky gut is one of the preconditions for developing autoimmune disease. (1) If you already have an autoimmune condition, leaving leaky gut unaddressed can cause your condition to progress and increase your risk of developing additional autoimmune diseases.

To learn more about this connection, listen to this episode of Take Back Your Health™ podcast with Dr. Alessio Fasano.

The important thing to understand is that gluten triggers this response in everyone, not just those with celiac disease or a diagnosed gluten sensitivity. Gluten has been linked to more than 55 diseases.(2) Modern wheat has also been hybridized and deaminated, meaning the gluten your body is exposed to today is structurally different from what previous generations ate, and your immune system does not recognize it.

Gluten Drives Chronic Inflammation

Once foreign particles escape through your leaky gut and enter your bloodstream, your immune system responds the only way it knows how: with inflammation. This is your body trying to protect you. The problem is that when you are eating gluten regularly, that inflammatory response never gets a chance to turn off.

Chronic inflammation is what drives you up the Autoimmune Spectrum. The more inflammation you have, the more dysregulated your immune system becomes. Over time, a chronically stressed immune system loses its precision. Instead of targeting specific invaders, it begins attacking indiscriminately, and your own tissues end up in the crossfire.

Research shows that eating gluten can elevate your gluten antibodies for months, meaning that even occasional gluten exposure, a few times a year, can keep your body in a near-constant state of inflammation. (3) This is why going gluten-free halfway does not work. It has to be complete.

Gluten Mimics Your Own Tissues

Beyond leaky gut and inflammation, gluten poses a specific and serious risk for those with autoimmunity due to a phenomenon called molecular mimicry.

Molecular mimicry diagram

Every time your immune system encounters an invader, it memorizes its structure so it can recognize and attack it in the future. The problem is that gluten's protein structure closely resembles several of your body's own tissues, particularly your thyroid. So when your immune system sends out antibodies to attack gluten that has slipped into your bloodstream through a leaky gut, it can mistakenly attack your thyroid tissue as well.

This is especially relevant if you have Hashimoto's or Graves'. Every time you eat gluten, you may be unknowingly triggering an immune attack on your own thyroid. The same concept applies to other cross-reactive foods, particularly casein in dairy, which has a similar molecular structure to gluten.

Removing gluten entirely gives your immune system the opportunity to stand down, stop the mistaken attacks, and begin to restore balance.

Learn about my personal journey with Graves’ disease on this episode of Take Back Your Health™ podcast.

How to Repair the Damage

Going gluten-free is the essential first step, and for many of my patients, it is the single most impactful change they make. Yet gluten-free alone is not always enough if your gut lining has already been compromised. That is why I also recommend actively working to repair your gut using the 4R approach: Remove, Restore, Reinoculate, and Repair.

The most important step in that final R, which is Repair. This pillar gives your gut lining the targeted nutritional support it needs to rebuild. My go-to for this is Leaky Gut Revive®, which contains L-glutamine, aloe vera, deglycyrrhizinated licorice, arabinogalactan, slippery elm, and marshmallow root. These nutrients work together to soothe and restore the integrity of your gut lining so that the tight junctions can close and the inflammatory cycle can finally begin to resolve. It also comes in a delicious Strawberry Lemonade flavor.

Healing your gut and going gluten-free are the first two pillars of The Myers Way® for good reason. Together, they create the foundation your immune system needs to stop attacking your own tissues and start functioning optimally again.

The Final Word on Gluten and Autoimmune Disease

If you have an autoimmune condition, the question is not whether to go gluten-free. It’s how soon can you start? 

I understand that this shift can feel challenging at first, especially when gluten is so common in everyday foods and social settings. Start by focusing on what you can enjoy rather than what you are removing. Build your meals around whole, nutrient-dense, AIP-compliant foods such as quality proteins, healthy fats, and a wide variety of vegetables. With time, your taste buds adapt, your cravings diminish, and most importantly, your body begins to respond. 

In AMMD™’s The Autoimmune Solution™ Protocol, you’ll find guides, meal plans, shopping lists, and high-quality physician-formulated supplements available to help you achieve this step-by-step. It’s not just about food; it's also about a lifestyle shift to take back your health!  

Many of my patients noticed improvements in energy, digestion, and mental clarity within just a few weeks. Stay consistent, be patient with the process, and remember that every gluten-free choice you make is a step toward calming your immune system and reclaiming your health.

Your immune system is ready to recover, so it’s time to give it the chance!



FAQs

  • What are the benefits of going gluten-free with autoimmune disease?
    Removing gluten from your diet can reduce chronic inflammation, help close the tight junctions of a leaky gut, and give your immune system the break it needs to stop attacking your own tissues. For many of my patients, going gluten-free is the single most impactful change they make in reversing their autoimmune condition.
  • What is the connection between gluten and autoimmune disease?
    Gluten triggers the release of zonulin, a protein that opens the tight junctions of your gut lining and creates leaky gut, one of the preconditions for developing autoimmune disease. Once your gut is permeable, gluten and other particles enter your bloodstream and drive the chronic inflammation that pushes you further along the Autoimmune Spectrum.
  • Is a gluten-free diet beneficial for all autoimmune conditions?
    Yes. While the gluten and autoimmune disease connection is most well-researched in Hashimoto's and Graves', gluten drives leaky gut and chronic inflammation regardless of which autoimmune condition you have. I recommend a completely gluten-free diet for every patient with any autoimmune condition.
  • What is molecular mimicry, and why does it matter?
    Molecular mimicry occurs when your immune system mistakes your own tissues for a foreign invader because their structures look similar. Gluten proteins closely resemble thyroid tissue, meaning that every time your immune system attacks gluten in your bloodstream, it can mistakenly attack your thyroid as well. This is particularly important if you have Hashimoto's or Graves'.
  • Does a gluten-free diet reduce inflammation?
    Yes. Research shows that gluten can elevate inflammatory antibodies for months after exposure, meaning even occasional gluten consumption can keep your body in a near-constant state of inflammation. A complete gluten-free diet, combined with gut repair support such as Leaky Gut Revive®, is the most effective way to break the inflammatory cycle and support your immune system in restoring balance.

Article Resources

  1. Zonulin and Its Regulation of Intestinal Barrier Function. Alessio Fasano. PubMed. 2012. Accessed on March 19, 2026.
  2. Gluten and Its Related Disorders. Hadjivassiliou et al. New England Journal of Medicine. 2002. Accessed on March 19, 2026.
  3. Gluten Causes Gastrointestinal Symptoms in Subjects Without Celiac Disease. Seidner et al. PubMed Central. 2015. Accessed on March 19, 2026.
Meet the Author

Amy Myers, MD

Dr. Myers is an accomplished, formally-trained physician who received her Doctorate of Medicine from Louisiana State University Health Science Center in 2005.
Along the way, she made it her mission to help those who've also been failed by the conventional medical system restore their own health and live their best lives.

Leave a Comment