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Autoimmune Thyroid Disease and AIP

Autoimmune Thyroid Disease is the most common cause of thyroid dysfunction in Australia, affecting around 10-15% of the population. The Autoimmune Protocol (AIP) is used to identify dietary triggers, reduce inflammation, and improve thyroid symptoms.

Autoimmune Thyroid Disease is the most common cause of thyroid dysfunction in Australia, affecting around 10-15% of the population.

What is the Thyroid?

The thyroid is a butterfly-shaped gland that is located in the front of your neck, just below the larynx (Adam’s apple). It is not visible when it is functioning properly.

The thyroid gland produces hormones that regulate many of your body’s functions including metabolism, growth, heart, muscle and digestive function, nervous system, temperature regulation, cognitive function and bone maintenance.

How does the Thyroid work?

The thyroid gland uses the amino acid tyrosine and iodine from the foods you eat to synthesise two main hormones which are carried to all the cells in the body.

These hormones are known as the Thyroid Hormones.

  • Triiodothyronine (T3)
  • Thyroxine (T4)

The thyroid gland produces around 20% of T3, the highly active form of the hormone, and 80% of T4, a prohormone which is converted to the active T3 form by specific enzymes in tissues such as the liver and kidneys.

The levels of T3 and T4 are maintained in the body through the release of the Thyroid Stimulating Hormone (TSH). The Pituitary gland, which is located at the base of your brain, responds to low levels of thyroid hormone in the blood by releasing TSH which tells your thyroid gland to increase thyroid hormone production.

In addition to TSH levels in the blood, the pituitary gland is regulated by the hypothalamus in the brain which releases TSH Releasing Hormone which tells the pituitary gland when to release TSH to stimulate the thyroid gland.

This complex system is known as the Hypothalamus-Pituitary-Thyroid Axis (HPT Axis) which functions to maintain normal levels of thyroid hormones circulating in the body.

What could go wrong?

When everything is functioning “normally”, the thyroid gland produces the right levels of thyroid hormones to support healthy metabolism and body function.

However, when the HPT Axis is disrupted, the thyroid may produce too much or too little thyroid hormones.

Thyroid function may be disrupted by a nutrient-poor diet, stress, trauma, environmental toxin exposure, viral or bacterial infection, gut dysbiosis, nutrient deficiencies, inflammation or autoantibodies.

Autoantibodies are associated with autoimmune thyroid disease (AITD), which is the most common cause of thyroid dysfunction.

What is Autoimmune thyroid disease?

AITD can be either Hasimoto’s or Graves’ Disease and both result in thyroid dysfunction.

Hashimoto’s Disease occurs when the body’s immune system attacks the thyroid gland causing increased inflammation and destruction of thyroid cells, resulting in a decrease of thyroid hormones (hypothyroidism).

When your thyroid is underactive it does not make enough thyroid hormone to support normal metabolism and body functions. Hypothyroid symptoms may include weight gain, constipation, joint or muscle pain, fatigue, feeling cold, thinning dry hair, sadness or depression, heavy menstrual bleeding etc.
Hypothyroidism affects more women than men.

Graves’ Disease occurs when the immune system stimulates the thyroid to produce too much hormone – hyperthyroidism.

When your body has too much thyroid hormone, the body’s processes speed up and cause symptoms including weight loss, rapid heartbeat, increased bowel movements or diarrhoea, increased sweating, anxiety or nervousness, sleep issues, trembling hands, fewer and lighter menstrual bleeds etc.

Autoimmune Thyroid Disease and other Autoimmune Conditions

Hashimoto’s Thyroiditis is the most prevalent autoimmune disease and is frequently associated with other autoimmune conditions.

AITD may occur concurrently with coeliac disease, rheumatoid arthritis, systemic lupus erythematous and Sjogren’s syndrome.

How is Thyroid dysfunction diagnosed?

Thyroid conditions can be difficult to diagnose as many of the symptoms are common to other medical conditions. However,  a detailed client and family history can often provide an indication that the thyroid needs to be tested.

Blood Tests:

TSH: High TSH indicates low thyroid function while low TSH indicates an overactive thyroid.

T3: the active form of the thyroid hormone

T4: the prohormone that becomes the active form through conversion in the liver and kidneys

Reverse T3 (rT3): an inactive form of T3 that cannot be used by the body. A high rT3 indicates an issue with T4 to T3 conversion.

Anti-thyroglobulin AB (TRAb) and Anti-TPO AB are thyroid antibodies that are elevated in autoimmune conditions such as Hashimoto or Graves’ disease.

Testing the full thyroid panel is very important in diagnosing thyroid conditions properly.


A thyroid ultrasound identifies whether there have been any structural changes such as the presence of nodules or cysts or enlargement of the thyroid gland.

Fine Needle Biopsy

A sample of cells may be collected from a nodule during the ultrasound to identify cells that may be cancerous.

Can AIP help manage Autoimmune Thyroid Disease?

The conventional treatment for AITD is through the prescription of medication to replace thyroid hormone in the case of Hashimoto’s Disease, or medication to suppress thyroid hormone for Graves’ Disease. Complementary treatment works side by side the medical treatment.

The Autoimmune Protocol (AIP) is used to identify dietary triggers, reduce inflammation, and improve thyroid symptoms. Several studies have shown that people with Hashimoto’s, continue to have debilitating symptoms even while taking thyroid medication. The AIP helps eliminate the symptoms the medication doesn’t address. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis (

In addition, nutritional supplements may be prescribed such as zinc, selenium, vitamin D, and iodine to support healthy thyroid function. Managing stress, improving sleep, and increasing physical activity are also important components of the AIP.

Read more about the AIP here: Healing Autoimmune Disease Naturally | The Nutrition Factor – Vicky Ellenport | Clinical Nutritionist Melbourne).

If you have been diagnosed with a thyroid disorder or an autoimmune condition and want to know more about managing AID naturally, please book in for a complimentary Discovery Session with Vicky Book Appointment ( to find out how AIP may be helpful for you.