In clinic, I often see women who are on thyroid medication, whose blood tests look “normal”, and who still feel tired, bloated, foggy and constipated. Medication replaces the hormone. It doesn’t address why the immune system is attacking the thyroid in the first place, and that is where the gut comes in.

How does the thyroid work?

Your thyroid is a small, butterfly-shaped gland at the front of your neck, just below your Adam’s apple. Its hormones help regulate almost every system in your body, including metabolism, energy, body temperature, heart rate, digestion, mood, brain function and bone health.

The thyroid uses iodine and the amino acid tyrosine from your diet to make two main hormones:

• T4 (thyroxine): about 80% of what the thyroid releases. T4 is a storage form that needs to be converted into T3 before your cells can use it.
• T3 (triiodothyronine): the active hormone. The thyroid makes a small amount directly, and most of your T3 is made from T4 in tissues like the liver, kidneys and gut.

Your brain controls how much hormone the thyroid makes. The hypothalamus releases thyrotropin-releasing hormone (TRH), which tells the pituitary gland to release thyroid stimulating hormone (TSH). TSH then tells the thyroid to produce more T4 and T3. This feedback loop is called the hypothalamic-pituitary-thyroid (HPT) axis.

This system can be thrown off by nutrient deficiencies, chronic stress, infections, environmental toxins, inflammation, gut dysbiosis and autoimmunity.

Hashimoto’s and Graves’ disease

There are two main types of autoimmune thyroid disease.

Hashimoto’s thyroiditis is the most common. The immune system attacks the thyroid, causing inflammation and gradual damage to thyroid cells, so over time the thyroid makes less hormone (hypothyroidism). Symptoms can include fatigue, weight gain, constipation, feeling cold, dry skin, thinning hair, joint and muscle aches, low mood and heavy periods. It is far more common in women.

Graves’ disease happens when antibodies switch the thyroid on, so it makes too much hormone (hyperthyroidism). Symptoms can include weight loss, a racing heart, loose bowels, sweating, anxiety, poor sleep, shaky hands and lighter periods.

Once you have one autoimmune condition, you’re more likely to develop another. Hashimoto’s often occurs alongside coeliac disease, rheumatoid arthritis, lupus and Sjögren’s syndrome.

The gut and thyroid connection

Researchers now talk about a “gut-thyroid axis”. Your gut and your thyroid affect each other in both directions, and when one is out of balance, the other usually is too.

Dysbiosis and leaky gut. People with Hashimoto’s and Graves’ tend to have different gut bacteria to people without thyroid disease. When the microbiome is out of balance, the gut lining becomes more permeable and lets bacterial fragments into the bloodstream. This keeps the immune system on alert and can make thyroid autoimmunity worse. I explain this in more detail in How Your Gut Microbiome Drives Inflammation in Autoimmune Disease.

Nutrient absorption. Your thyroid depends on selenium, zinc, iron and iodine, and your gut bacteria play a key role in absorbing them. You can eat well and still be low if your gut isn’t absorbing properly.

Hormone recycling. Gut bacteria help reactivate thyroid hormone that the liver has packaged up for removal, so more of it goes back into circulation.

Medication absorption. Thyroid medication is absorbed in the small intestine. Coeliac disease, H. pylori infection, low stomach acid and inflammatory bowel conditions can all reduce how much you absorb. If your dose keeps creeping up, your gut is worth checking.

SIBO. A slow thyroid slows the gut, and a sluggish gut is a set-up for small intestinal bacterial overgrowth. A 2025 study found people with hypothyroidism were about twice as likely to develop SIBO, and the risk was higher again with autoimmune thyroiditis. This is one reason bloating and constipation are so common with Hashimoto’s.

Coeliac disease. Coeliac disease is more common in people with autoimmune thyroid disease. It damages the gut lining, affects nutrient and medication absorption, and is easy to miss because the symptoms can be subtle.

Testing: look at the thyroid and the gut

Thyroid symptoms overlap with so many other conditions that they’re easy to miss. A detailed personal and family history is often the first clue that the thyroid needs testing.

A full thyroid panel, not just TSH, should include:

• TSH: high usually means an underactive thyroid, low usually means an overactive one
• Free T4 and free T3: how much hormone is available, and how well you’re converting T4 into active T3
• Thyroid peroxidase antibodies (TPO Ab) and thyroglobulin antibodies (TgAb): raised in Hashimoto’s
• TSH receptor antibodies (TRAb): raised in Graves’ disease

Your doctor may also order a thyroid ultrasound to check for nodules or enlargement.

Gut testing is where we find out what’s driving the immune response:

• Microbiome stool testing to look at diversity, beneficial bacteria, inflammatory species and gut barrier markers
• SIBO breath testing if you have bloating, gas, constipation or reflux
• Coeliac screening through your GP, before removing gluten, because the blood test needs gluten in your diet to be accurate
• Nutrient levels such as iron studies, vitamin D and zinc

Test don’t guess. Two people with the same antibody levels can have very different things going on in their gut microbiome.

Where does AIP fit?

The Autoimmune Protocol (AIP) is an elimination and reintroduction diet. For a period of time, it removes foods that can trigger an immune response in some people (gluten and other grains, dairy, eggs, legumes, nightshades, nuts, seeds, refined sugar, alcohol and processed foods). The focus is on vegetables, quality protein and healthy fats. Foods are then brought back one at a time so you can see what you actually react to.

In a 10-week study of 17 women with Hashimoto’s, AIP significantly improved quality of life and symptoms, and lowered a marker of inflammation (hs-CRP). Thyroid antibodies didn’t change in that time. It’s a small study, but it supports what I see in practice. People often feel much better even when their medication dose stays the same.

AIP is a short-term tool, and the reintroduction phase is the most important part. Microbiome testing shows which beneficial bacteria are missing or low, which helps me prioritise the foods to bring back first. Fibre is usually the most important, because it feeds the bacteria that produce anti-inflammatory compounds like butyrate. Staying restricted for too long starves these bacteria, so a guided reintroduction is important.

Nutrients that support the thyroid

• Selenium: an analysis of 35 studies found selenium lowered TPO antibodies in people with Hashimoto’s. Brazil nuts are a rich source, but the amount varies a lot between nuts, so supplements should be dosed carefully.
• Zinc: needed to make thyroid hormone and convert T4 to T3.
• Vitamin D: helps regulate the immune system, and low levels are common in autoimmune disease.
• Iron: low iron stores can slow thyroid hormone production.
• Iodine, with care: the thyroid needs iodine, but too much can trigger or worsen Hashimoto’s. Don’t take iodine supplements or kelp without professional advice.

Stress, sleep and regular movement all matter too. Chronic stress affects both your thyroid and your gut, so it’s part of any plan I put together.

Ready to look deeper?

If you’ve been diagnosed with Hashimoto’s or Graves’ and you’re still struggling with fatigue, bloating, constipation or brain fog, your gut is a good place to start. I combine microbiome testing, SIBO breath testing (when needed) and a review of your pathology, then build a plan around what’s actually going on for you.

Book a discovery call here.

If you’re ready to understand your gut health a little better, follow along on Instagram. 💚

REFERENCES

Abbott RD, Sadowski A, Alt AG. Efficacy of the autoimmune protocol diet as part of a multi-disciplinary, supported lifestyle intervention for Hashimoto’s thyroiditis. Cureus. 2019;11(4):e4556. doi:10.7759/cureus.4556. https://doi.org/10.7759/cureus.4556

Busto Silva I, Puig-Domingo M. The impact of thyroid disorders on the gut microbiome: emerging mechanisms and clinical relevance. Arch Endocrinol Metab. 2026;70(spec issue 1):e250075. https://pmc.ncbi.nlm.nih.gov/articles/12679698

Hughes K, Eastman CJ. Hashimoto’s thyroiditis: how to spot the diagnosis and how to manage it. Med Today. 2017;18(9):27-32. https://medicinetoday.com.au/mt/2017/september/feature-article/hashimotos-thyroiditis-how-spot-diagnosis-and-how-manage-it

Huwiler VV, Maissen-Abgottspon S, Stanga Z, et al. Selenium supplementation in patients with Hashimoto thyroiditis: a systematic review and meta-analysis of randomized clinical trials. Thyroid. 2024;34(3):295-313. doi:10.1089/thy.2023.0556. https://pmc.ncbi.nlm.nih.gov/articles/PMC10951571/