Celiac Disease and Thyroid Disease: Connect the Dots to Feeling Better

When Gluten-Free Isn’t Enough

Have you been diagnosed with celiac disease and gone gluten-free, yet things still aren’t quite right? You experience fatigue, brain fog, muscle and joint pain. Maybe you’re cold much of the time or you've noticed dry skin and brittle nails.

If so, you're not alone.

This is the story of how I discovered the celiac disease and thyroid disease connection. And most importantly, how that discovery led me to solve the mystery of stubborn symptoms. 

It’s my personal experience – not medical advice – but if you recognize yourself in this story, maybe it’s worth a conversation with your doctor.

Living with Celiac Disease — Symptoms That Didn’t Go Away

When I first received my celiac diagnosis, I was perplexed. I wasn’t underweight. I didn’t feel sick after eating bread or pasta. But as I learned more about celiac symptoms, I started connecting the dots backwards though my life. It wasn't just about upset stomach and diarrhea. 

• As my skin problems started clearing up, I learned about dermatitis herpetiformis (dh) and its link to celiac disease. 
• When I read about the connection between celiac and miscarriage my four lost pregnancies suddenly made sense.
• I learned how celiac disease can cause lactose intolerance, low iron and chronic low energy. 

The examples kept piling up as the lights popped on one by one.

My thyroid experience was similar. Even after years on a strict gluten-free diet I was still having symptoms:

• Dairy and eggs caused problems.
• My muscles ached and my joints felt inflamed.
• Fatigue made climbing the stairs feel like climbing a mountain.
• I had diarrhea after meals with no clear trigger.
• I experienced heart palpitations, dizziness, and brain fog.
• I developed random hives with no obvious cause.

The Moment I Knew for Sure Something Wasn't Right

My turning point came on a Tampa vacation, when a restaurant meal ended with a call to the paramedics. This was the moment I knew I needed answers.

I’d just finished an appetizer of fresh mussels and a cider when the room started to spin and my heart began racing. I felt dizzy, shaky, and scared. I tried to make myself throw up, but couldn’t. I was sure I was having a serious allergic reaction.

By the time the paramedics arrived, my heart rate was settling and I appeared fine. They suggested it may have been an allergic reaction and recommended Benadryl. Once I took it, the episode faded as quickly as it had started — l was confused and determined.

Things I Tried – That Didn’t Work

Armed with my growing list of symptoms, I turned to the internet – which as you know, can be a nest of vipers.

I read that keto can help with joint inflammation, so I tried that. I lost some weight, but no help for the joints.

I read that sulfites and histamines could cause heart palpitations and some food intolerances. I eliminated those to no avail. I kept Benadryl in my purse in case of a replay of the Tampa experience.

Frustrated and desperate, I asked ChatGPT to help me figure out what might be going on.

It had some interesting suggestions:

• SIBO (Small Intestine Bacterial Overgrowth)
• Mast Cell Activation Syndrome
• Other autoimmune conditions, including Hashimoto’s thyroiditis or autoimmune gastritis

I knew I couldn't figure this out on my own. I needed a doctor who could run tests and give me a diagnosis.

Working With the Medical System - Conventional vs Functional Medicine

If you have celiac disease you know how frustrating it can be to deal with the medical system - long waits, misdiagnoses - you feel dismissed and invisible.

I had made detours into alternative medicine with mixed results. A regimen of apple cider vinegar and honey ended my miscarriage streak but other treatments like hydrogen peroxide infusion and applied kinesiology were dead ends.

Conventional medicine had failed me too. Dermatitis Herpetiformis was misdiagnosed as contact dermatitis. My lactose intolerance and frequent miscarriages were never connected to celiac disease.

So how was I going to approach this new problem?

I suspected I might need a functional medicine doctor, but they’re expensive and not covered by our provincial medical plan. So, I decided to go as far as I could in the conventional system then, if necessary, I’d spend the money on a functional practitioner.

I took my symptom list to my GP. He referred me to an Internal Medicine (IM) specialist and an allergist.

The allergist couldn't help. The IM specialist was a very different story!

The Diagnosis: Hashimoto’s Thyroiditis

The specialist reviewed my labs and my long list of symptoms, then asked me what my goals were.

“I just want to not feel like crap all the time” was my tearful answer.

He nodded and went on to explain “subclinical hypothyroidism.”¹

My TSH had been slightly elevated for years, but I'd always been told, “It’s only a little high, we don’t treat that.” When I pushed, I was warned that treatment meant lifelong medication. "You don’t want that, do you?"

This doctor had the experience and the nuance. Yes, my TSH was only mildly elevated and my T4 (another thyroid hormone) was normal. But combined with my symptoms this was enough for him to suspect Hashimoto’s - an autoimmune thyroid condition. 

His reasoning was straightforward:

• I had celiac disease – celiac and Hashimoto’s often occur together.
• My TSH had been persistently elevated, even if only slightly.
• I had classic thyroid symptoms: fatigue, muscle and joint pain, always cold.

He ordered more blood tests: anti-thyroid peroxidase (anti-TPO) and anti-thyroglobulin antibodies and started me on a low dose of levothyroxine. I was to come back in six months and if the meds helped, I had my diagnosis. 

The meds helped – a lot!

Why Celiac Disease and Hashimoto’s Often Occur Together

Now that I had my diagnosis, I needed to know why. Why did I have both celiac disease and Hashimoto’s? Was this just bad luck, or is there a connection?

Both Conditions Are Autoimmune

Celiac disease and Hashimoto’s are both autoimmune conditions. That means the immune system attacks the body’s own tissues.

In celiac disease, the target is the small intestine. In Hashimoto’s, it’s the thyroid.

Once you have one autoimmune disease, the risk of developing another increases. Doctors call this autoimmune clustering. Celiac disease and autoimmune thyroid disease are one of the most common pairings.²

Shared Genetic Tendencies

There’s also a genetic link.

Most people with celiac disease carry specific immune-related genes (HLA-DQ2 and/or HLA-DQ8). These genes affect how the immune system distinguishes between your body and outside invaders.

The same genes are associated with Hashimoto’s.³

Understanding this helped me to make sense of my thyroid diagnosis.

Connecting The Dots in Reverse: Symptoms that Improved with Thyroid Meds

As the months on levothyroxine passed, I started checking symptoms off my list:

• Joint inflammation eased – I could kneel on the floor to play with my grandson.
• Muscle aches faded – that feeling of hurting everywhere all the time was going away.
• Chronic fatigue lifted – I still love naps, but no longer feel like I need one.
• Hives, heart palpitations, diarrhea – all gone. 

 Unexpected Symptoms that Turned Out to Be Thyroid Related

When I noticed improvements in things that I'd just come to accept, I began to wonder if this went deeper than I'd realized. 

These symptoms aren't always listed as signs of hypothyroidism, but they improved after I started the medication.  With a little more research, I found connections.

• Thin, splitting nails with vertical ridges ⁴
• Thinning of the outer third of the eyebrows⁵
• Heavy periods and uterine fibroids ⁶
• Alcohol intolerance⁷
• Gallstones ⁸
• Food intolerances (casein and eggs)⁹

What I Wish I Knew Earlier About Celiac Disease and Thyroid Disease

As with my celiac diagnosis, I wish one of the many doctors I’ve seen had connected the dots between my symptoms and my thyroid. And like with my celiac diagnosis, if they had, I’d have been spared years of discomfort.

So, what advice can I offer:

• Your symptoms aren’t “in your head.” Keep pushing until you have answers.
• TSH even slightly outside of normal could be a sign of thyroid trouble.
• If going gluten-free doesn’t fix everything, consider another autoimmune condition.
• Food intolerances can sometimes point to thyroid issues.
• Track your symptoms and get help. Don’t expect to fix this on your own.
• Get a pill organizer.  It's important not to miss your thyroid meds - this helped me a lot.

Remember, this is just my personal experience, but if you have stubborn symptoms, don’t dismiss them. There may be an answer, you just have to be persistent. All the best!

8. Shomon, M. (2025, December 7). Hashimoto’s, hypothyroidism, and your gallbladder: Paloma health. Paloms. https://www.palomahealth.com/learn/hashimotos-hypothyroidism-gallbladder-pain#:~:text=Even%20subclinical%20hypothyroidism%20can%20impact,patients%20presenting%20with%20these%20symptoms.