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/

The process of getting an AID diagnosed can be so long, drawn out and frustrating that it is not uncommon for people with AID to be labelled a hypochondriac – a person who fears they are living with a serious, undiagnosed medical condition despite diagnostic tests showing that there is nothing wrong with them – especially in the early stages of illness.

On average, a person will see 5 doctors over the course of several years to finally receive an autoimmune disease diagnosis.

Autoimmune Disease Symptoms

While different autoimmune diseases affect different organs and systems in the body, what they all have in common is that they occur when the body’s immune system mistakenly attacks its own cells.

Autoantibodies are immune proteins that target the body’s own healthy tissue when the immune system fails to distinguish between “self” and “non-self”.

The continual attack on the body’s cells causes inflammation and sufficient tissue damage that symptoms of disease begin to emerge.

People with an autoimmune disease may describe long-term struggles with a wide range of symptoms such as: fatigue, gastrointestinal issues, joint pain, recurring infections, skin problems, allergies, migraines, unexplained weight changes, anxiety/depression, low/high blood pressure and more.

Why does it take so long to get an autoimmune disease diagnosis?

• Common, non-specific symptoms. The symptoms of autoimmune conditions vary widely and are generally non-specific, that is, symptoms that may describe any one of a variety of conditions. In the early stages of the illness people will usually present to their doctor or health professional for help with one, primary complaint (e.g., recurring urinary tract infection or persistent acne or inability to lose weight) and many of the other symptoms they are experiencing do not get mentioned. It is not until the practitioner has a full picture of ALL the symptoms, together with a full health history, that the connection between the symptoms becomes clearer, and that the possibility of an AID may become apparent.
• Remission/flare pattern. It is possible for an AID to enter a period of remission, where a person may have very mild symptoms, or even be asymptomatic, for a period. At this time, for an undiagnosed person, it may seem that the illness has resolved and is all but forgotten about. However, when triggered, AID can enter a flare phase when symptoms return suddenly and severely leaving the sufferer exhausted, depleted and in pain.
• Asymptomatic or slow to develop signs and symptoms. Not all Autoimmune Diseases cause symptoms immediately. It is possible to live with an AID for many years before symptoms become apparent or before an incident occurs that leads to an AID diagnosis. For example, ankylosing spondylitis symptoms may develop very gradually and often goes undiagnosed for several years, before it becomes visible on an x-ray. Likewise, Type 1 diabetes involves a gradual destruction of the pancreatic beta cells and it is only diagnosed once 90% of the cells have been destroyed.
• Co-Conditions. It is possible to have more than one AID, in fact having one AID increases the chances of you developing another. When there is more than one AID present, it is possible for one to mask the other. For example you may have been diagnosed with Rheumatoid Arthritis, but in actual fact you also may have Coeliac Disease, the symptoms of which contribute to joint pain, but remains undiagnosed if there are no other obvious symptoms.
• Every person is different and, with AID affecting a wide variety of organs and causing such varied symptoms, each presentation of each condition can be different. It is possible that two people may be diagnosed with the same condition with very different symptoms. Alternatively, two people with the same symptoms may be affected by different conditions.

Risk Factors for Autoimmune Disease.

Certain risk factors are known to increase the chances of developing an autoimmune disorder. The presence of any one of these risk factors, along with a description of all the symptoms, can help to get closer to an AID diagnosis.

• Genetics. While members of the same family may suffer from different autoimmune conditions, a predisposition to autoimmune disease does appear to run in families.
• Excess weight is associated with increased risk of developing an AID that affects the joints such as Rheumatoid and Psoriatic Arthritis. In addition, adipose tissue, or fat, secretes pro-inflammatory compounds that cause low-grade chronic inflammation and dysregulation of the immune system.
• Smoking. The toxic chemicals that are released when tobacco is burned impacts the immune system by causing inflammation, suppressing immune function, and stimulating the production of autoantibodies.
• Certain medications. The side effects of some pharmaceuticals that are widely used daily can have side effects that involve the immune system and can lead to an autoimmune reaction.
• Infection with a virus, such as Epstein Barr Virus (EBV), or bacteria, such as Streptococcus, can turn on genes that impede the immune system’s ability to differentiate between self and non-self, initiating an autoimmune reaction.

Are there tests for Autoimmune Disease?

There is no single test to diagnose AID but rather a selection of markers in blood or urine samples which, when put together with the presenting symptoms can lead to an AID diagnosis.

• Autoantibodies: The presence of autoantibodies may indicate an autoimmune disease.
  • Antinuclear Antibody (ANA) Test. A high level of these autoantibodies may be used to diagnose a systemic AID such as lupus and may be used to rule out other conditions with similar symptoms
  • Rheumatoid Factor (RF) is used to diagnose Rheumatoid Arthritis (RA). A positive test for RF differentiates RA from osteoarthritis and other connective tissue disorders.
  • Thyroid Antibody test (TPO) is used to diagnose Hashimoto’s or Graves disease in conjunction with other thyroid testing.
• Inflammation Markers: C-Reactive Protein (CRP) and Erythrocyte Sedimentation Rate (ESR) are used to detect the presence of inflammation, a common characteristic symptom of all AID’s.
• X-Rays, Gastroscopes and Biopsies: may be used to confirm or support an AID diagnosis.

Why do you need a diagnosis?

• Many people suffer with symptoms for many years and finally having a diagnosis can be a validation that it was not just in their mind.
• Knowing what is causing your symptoms allows your health practitioner to tailor a treatment plan specific to your needs.
• Having a diagnosis means that your health care team can anticipate, and help to reduce the risk, of disease progression or future complications.
• It helps you educate yourself and gain a better understanding about your condition and how to manage it.
• It reminds you that you are not alone, and that you can reach out and connect with others with the same condition so that you may support one another.

You have been diagnosed with an autoimmune disease, so what now?

Once you receive an AID diagnosis, the treatment approach is up to you. As there is no proven cure for AID, treatment is aimed at improving symptoms and promoting remission.

One option is the conventional medicine approach which prescribes pharmaceutical medications to manage symptoms and induce remission.

The other option is the natural medicine approach which aims to determine the underlying cause of your AID and to tailor a treatment plan to improve your symptoms and reduce the frequency of flare-ups.

As a natural medicine practitioner Vicky works in conjunction with your medical team, using a holistic approach to managing AID that encompasses thorough testing, identification of nutritional deficiencies, lifestyle and dietary recommendations and stress management techniques.

If you have been struggling with a long-term, undiagnosed health issue, or if you have recently been diagnosed with an AID, book in for a complimentary Discovery Session with Vicky to discuss the best options for managing your health.