Celiac disease and gluten sensitivity have strong connections to autoimmune conditions, including Hashimoto’s hypothyroidism, and play a major role in gut health and immune system dysfunction. Many people with hypothyroidism or other autoimmune diseases don’t realize that gluten could be a root trigger in their condition.
Here’s how gluten contributes to autoimmunity and leaky gut, and why removing it may be essential for healing.
1. Celiac Disease: An Autoimmune Reaction to Gluten
Celiac disease is an autoimmune disorder in which the immune system attacks the small intestine in response to gluten, a protein found in wheat, barley, and rye.
In people with celiac disease, gluten triggers an immune attack against the gut lining, causing chronic inflammation and damage to the intestinal walls.
This leads to nutrient malabsorption, which can contribute to deficiencies in iron, selenium, zinc, B vitamins, and vitamin D—all of which are crucial for thyroid health and immune function.
Celiac disease also increases the risk of other autoimmune diseases, including Hashimoto’s, rheumatoid arthritis, and type 1 diabetes.
Key takeaway: Celiac disease is not just a digestive disorder—it’s an autoimmune condition that can trigger inflammation throughout the body.
2. Gluten & Non-Celiac Gluten Sensitivity in Autoimmunity
Even if you don’t have celiac disease, gluten can still contribute to autoimmune diseases through non-celiac gluten sensitivity (NCGS).
Some people experience systemic inflammation, brain fog, joint pain, and digestive issues after consuming gluten, even without celiac disease.
Gluten has been linked to increased intestinal permeability (leaky gut), which can trigger or worsen autoimmune conditions.
Many individuals with Hashimoto’s, lupus, multiple sclerosis, and rheumatoid arthritis experience improvement in symptoms after removing gluten, even if they don’t have celiac disease.
Key takeaway: Even without celiac disease, gluten may trigger inflammation and autoimmune flares in sensitive individuals.
3. Gluten & Leaky Gut: How It Weakens the Gut Barrier
What Is Leaky Gut?
Your gut lining acts as a protective barrier, keeping toxins, bacteria, and undigested food particles from entering your bloodstream. When the gut lining becomes damaged or hyperpermeable, unwanted substances can "leak" into the bloodstream, triggering inflammation and autoimmune responses.
Gluten increases zonulin levels, which makes the gut lining more permeable.
Zonulin is a protein that controls the tight junctions between gut cells.
When zonulin is activated (by gluten or infections), these junctions loosen, allowing large molecules and toxins to pass through the gut wall and enter the bloodstream.
This triggers the immune system to attack these foreign invaders, leading to chronic inflammation and a higher risk of autoimmune disease.
Leaky gut fuels the autoimmune cycle.
Once the gut barrier is compromised, the immune system becomes hyperactive, increasing the risk of attacking the body’s own tissues, including the thyroid, joints, and nervous system.
Key takeaway: Gluten contributes to leaky gut by increasing zonulin levels, which weakens the gut barrier and triggers inflammation.
4. The Connection Between Gluten, Hashimoto’s, and Autoimmunity
People with Hashimoto’s have a significantly higher rate of celiac disease and gluten sensitivity.
Up to 16% of people with Hashimoto’s have celiac disease (compared to 1% of the general population).
Gluten antibodies often cross-react with thyroid tissue, meaning the immune system mistakes thyroid cells for gluten, attacking the thyroid in the process.
Removing gluten can lower thyroid antibodies and inflammation.
Studies have shown that a gluten-free diet can reduce thyroid antibody levels in people with Hashimoto’s.
Many patients report improvements in energy, brain fog, digestion, and thyroid function after cutting out gluten.
Key takeaway: Gluten has been linked to Hashimoto’s due to its ability to trigger an immune response that attacks the thyroid. Removing gluten may reduce inflammation and slow disease progression.
5. How to Heal Autoimmune-Related Gut Damage
Instead of just eliminating gluten, it’s important to actively heal the gut to restore proper function and prevent future autoimmune flares.
Step 1: Remove Gut Irritants
Eliminate gluten (and possibly dairy & soy, which can also trigger autoimmunity).
Reduce processed foods, refined sugars, and artificial additives, which feed harmful gut bacteria.
Step 2: Repair the Gut Lining
Collagen & zinc carnosine – Supports gut repair and strengthens the intestinal lining.
L-glutamine – An amino acid that helps rebuild the gut barrier.
Vitamin A – Essential for mucosal healing and immune balance.
Step 3: Restore Healthy Gut Bacteria
Add probiotic-rich foods (fermented veggies, kefir, sauerkraut) or high-quality probiotics to support microbiome balance.
Increase fiber from vegetables to feed beneficial bacteria.
Step 4: Reduce Inflammation & Support Immune Balance
Omega-3s – Reduce autoimmune inflammation.
Vitamin D – Essential for immune function; get tested to optimize levels.
Selenium & magnesium – Help regulate the immune response and thyroid function.
Final Thoughts: Should You Go Gluten-Free for Autoimmune Health?
If you have celiac disease, Hashimoto’s, or any other autoimmune condition, there is strong evidence that removing gluten can help lower inflammation, reduce autoimmune attacks, and support gut healing. Since gluten contributes to leaky gut, fuels inflammation, and can cross-react with the body's tissues, going gluten-free may be a powerful tool for improving autoimmune symptoms.
That said, a gluten-free diet alone is not enough—true healing comes from:
Healing the gut
Balancing the immune system
Addressing nutrient deficiencies
Managing stress & lifestyle factors
By taking a comprehensive, root-cause approach, you can support healing from the inside out and drastically improve your health.
Disclaimer
This post is for informational and educational purposes only and is not intended to diagnose, treat, cure, or prevent any disease or medical condition. The information provided is not a substitute for professional medical advice. Always consult with a qualified healthcare provider before making any changes to your diet, lifestyle, supplements, or treatment plan.
The author and publisher of this content are not liable for any adverse reactions, effects, or consequences resulting from the use of any information provided. Individual health needs vary, and what works for one person may not be suitable for another.
If you have a medical concern, please seek guidance from a licensed medical professional.
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