How to Treat Thyroid Autoimmunity with Naturopathy


Blue butterfly representing thyroid health awareness

Have you been:

  • diagnosed with low thyroid function (hypothyroidism)

  • told you are in the early stages of low thyroid function (subclinical hypothyroidism)?

  • told you have elevated thyroid antibodies?

If you have answered yes to any of the above questions, you may have Hashimoto’s thyroiditis, the most common cause of low thyroid function in Australia.


What is Hashimoto’s thyroiditis?

Hashimoto’s thyroiditis is an autoimmune condition where your immune system produces antibodies that attack your thyroid gland over time. As the thyroid gland becomes more damaged, less thyroid hormones can be produced, leading to low thyroid function.

You may have been experiencing low thyroid function symptoms of weight gain, brain fog, and fatigue for a long time and been repeatedly told that your thyroid ‘is fine’.

However, your GP has probably only been testing for one hormone, thyroid stimulating hormone (TSH) and if that level is within range, no further investigation is usually made.

Your GP does not routinely test for the markers of Hashimoto’s thyroiditis, elevated thyroid antibodies TPOAb and TgAb, and even if you have been tested you may not have been told you have Hashimoto’s thyroiditis by your GP. This is because there is no conventional medical treatment for thyroid autoimmunity.

A GP’s treatment plan for low thyroid function caused by Hashimoto’s thyroiditis is to monitor TSH levels over time. A GP will only give a diagnosis of hypothyroidism (low thyroid function) and prescribe thyroid hormone replacement once TSH levels fall outside of the ‘normal’ range.

Once diagnosed, you may not feel much better after starting thyroid hormone replacement, such as thyroxine. This is because Hashimoto’s thyroiditis is actually an immune disease, not a thyroid disease. Whilst thyroid hormone replacement replaces the hormones your thyroid can no longer produce and is essential for your health, it does not treat your dysfunctional immune system that gradually destroys your thyroid tissue.

To reduce your symptoms of diagnosed low thyroid function, you should take thyroid hormone replacement as well as identify and treat the cause, thyroid autoimmunity.


How to do I find out if I have Hashimoto’s thyroiditis?

If you already have a low thyroid function diagnosis, ask your naturopath or GP to test for thyroid antibodies, TPOAb and TgAb. If one or both is above the reference range, you have Hashimoto’s thyroiditis. Treating the autoimmune attack against your thyroid gland will help to alleviate your low thyroid function symptoms.

In the early stages of Hashimoto’s thyroiditis prior to a low thyroid function diagnosis, you may still have normal TSH levels or what is called subclinical low thyroid function (TSH levels consistently at the very top end of the reference range).

If you have low thyroid function symptoms but keep getting told your TSH is not high enough to warrant thyroid hormone replacement (thyroxine), you should still test for thyroid antibodies. Please mention any family history of thyroid condition and autoimmune conditions such as type 1 diabetes, coeliac disease, and rheumatoid arthritis to your naturopath or GP to encourage them to order the testing.

If you have elevated thyroid antibodies, you have Hashimoto’s thyroiditis. In this early stage, you have a great opportunity to work on reducing the antibody attack on your thyroid gland. By slowing the progression of autoimmunity, you can help your thyroid gland to continue to produce adequate levels of thyroid hormones, which will help to reduce your low thyroid function symptoms.


Why does Hashimoto’s thyroiditis occur?

The following factors are often present in autoimmunity:

  • a genetic predisposition

  • environmental trigger/s

  • intestinal permeability (leaky gut)

Autoimmunity can be hereditary

You may have family members who have Hashimoto’s thyroiditis or Graves’ Disease, or other autoimmune diseases like coeliac disease, Sjogren’s syndrome, or rheumatoid arthritis.

However, just because you have a genetic predisposition, does not mean you will necessarily develop an autoimmune condition. Environmental trigger/s and leaky gut often need to be present for autoimmunity to develop.

Environmental triggers of autoimmunity include:

  • nutrient deficiencies

  • toxin exposure

  • chronic infections

  • prolonged stress

  • hormonal changes.

Intestinal permeability (leaky gut)

Leaky gut can also need to be present to trigger autoimmunity. This occurs when your gut lining gets damaged and allows undigested proteins, bacteria, and toxins to enter the blood stream. The immune system then sends out antibodies to attack them. Unfortunately, peptides from bacteria and proteins found in common foods look very similar in structure to our body’s cells. In people with a genetic predisposition to autoimmunity, a case of molecular mimicry can occur where their immune system gets confused and accidently begins to attack their body’s tissues too. In the case of Hashimoto’s thyroiditis, the immune system produces antibodies which attack the thyroid gland.


How do I treat Hashimoto’s thyroiditis?

To effectively treat Hashimoto’s thyroiditis, you need to remove environmental triggers and identify and treat the cause/s of leaky gut. This can help to slow down the autoimmune attack on your thyroid gland to reduce your low thyroid function symptoms.


How do I remove environmental triggers?

Correct nutritional deficiencies

Selenium helps to reduce thyroid antibody and TSH levels, protect the thyroid against inflammation and oxidative damage, and support healthy immune function.

You can ask your naturopath or GP for a blood test to check selenium levels. If you are deficient, you may benefit from supplementation.

A safe daily dose of selenium is 150mcg and the Therapeutic Goods Administration (TGA) warns that selenium can be toxic in higher doses. It is essential to check all of the supplements you are taking to ensure you are not exceeding the total daily dose of 150mcg.

You want to aim for your levels to be in the top end of the reference range and you should retest your levels in 12 weeks to see if you have achieved this.

Studies have shown that Vitamin D deficiency is linked to the development of thyroid antibodies and that supplementation can reduce their levels.

You can ask a naturopath or GP to test your Vitamin D levels and supplement, if deficient. The reference range is between 50–150 nmol/L, however with autoimmunity you want to aim for the higher end of the range, between 100–150 nmol/L.

1000IU of Vitamin D taken for three months will raise your levels by 25 nmol/L. For example, if your Vitamin D levels are current 50 nmol/L, you need to take 4000IU of Vitamin D daily for three months to reach a level of 150nmol/L.

Be sure to get a follow up blood test after three months of supplementation to ensure you have met your target. Don’t continue to take a high level of Vitamin D once you have reached your target as Vitamin D is fat soluble and can be toxic in large amounts. Please refer to a naturopath or pharmacist who can prescribe a safe maintenance dosage for you.

Reduce toxin exposure

The thyroid gland is very susceptible to damage from toxins and toxins are also a major trigger of thyroid autoimmunity. Reduce toxin exposure by:

  • reducing alcohol and quitting smoking

  • reducing exposure to pesticides by buying organic fruit and vegetables or reducing the Dirty Dozen (fruits and vegetables with high levels of pesticide residue) and consuming more of the Clean Fifteen (fruits and vegetables with lower levels of pesticide residue)

  • reducing your consumption of large fish which can contain high amounts of mercury and PCBs, including tuna, shark, and swordfish. Swap for smaller fish, like sardines and anchovies

  • buying cookware free of heavy metals and ‘forever’ chemicals. The Solidteknics nickel free stainless steel ‘NONI’ range and wrought iron ‘AUS-ION’ range, pictured below, are safer choices

  • filtering your drinking water

  • avoiding mould exposure as much as possible by treating water damage in the home and keeping bathrooms well-ventilated to reduce mould formation

  • avoiding bisphenol A (BPA) found in some canned foods, plastic drinking bottles and food storage containers, and EFTPOS receipts. Have more fresh, dried or frozen food in replacement of canned food. Replace plastic drinking bottles and food storage containers with glass or stainless steel versions. Sign up to get receipts sent electronically.

Solidteknics AUS-ION frying pans

Solidteknics AUS-ION frying pans are a safer cookware choice

Eradicate chronic infections

Viral infections like Epstein Barr virus (EBV) and bacterial infections such as Helicobacter pylori can both trigger autoimmunity through the molecular mimicry process that I detailed earlier.

You can ask your naturopath or GP to order a blood test for EBV and a breath test for H. pylori. If you have either of these infections, your health practitioner can give dietary and lifestyle advice as well as recommend herbal/nutritional supplements and/or pharmaceutical medication to eradicate the infection.

Address stress

Chronic stress can both trigger and drive Hashimoto’s thyroiditis and stress management techniques can be helpful in treating autoimmunity.

Supporting general health by implementing a healthy diet and exercise regime and improving sleep hygiene can help reduce physical stress on the body.

Seeking social support through trusted friends, family, and support groups and/or professional support from a counsellor or a psychologist can help to reduce mental and emotional stress.

Practising mindfulness techniques including meditation, progressive muscle relaxation, and diaphragmatic breathing can help reduce levels of the stress hormone, cortisol.

Balance hormones

Women are up to ten times more likely to develop Hashimoto’s thyroiditis than men. This is thought to be due to the fluctuations of oestrogen and progesterone throughout a woman’s life. Thyroid autoimmunity is often triggered at times of hormonal shift, including puberty, pregnancy, post-partum, and in perimenopause. It is also common for women with Hashimoto’s thyroiditis to be misdiagnosed or underdiagnosed, especially around these times.

For example, a woman who has just had a baby could have her Hashimoto’s thyroiditis symptoms of low mood, fatigue and brain fog misdiagnosed as post-partum depression or dismissed as ‘just part of being a mother of a newborn’. A women going through perimenopause could have her symptoms of weight gain and low mood attributed to this time of hormonal change, rather than the underlying cause, thyroid autoimmunity.    

As a naturopath, I can order a saliva hormone test that measures the levels of your reproductive hormones, oestrogen, progesterone, and testosterone. If your hormones are out of the normal range, I can devise a treatment plan to help restore hormone balance, including dietary and lifestyle advice as well as nutritional or herbal medicine. By balancing your reproductive hormones, you can reduce your risk of triggering autoimmunity as well as reduce reproductive hormone imbalance symptoms, including period problems and premenstrual syndrome (PMS). 


How do I treat leaky gut?

Treatment of leaky gut involves identifying and treating the following potential cause/s:

  • food sensitivities

  • intestinal infections

  • gut dysbiosis

  • nutrient deficiencies.

Remove food sensitivities

The protein from gluten, gliadin and the protein from cow’s dairy, A1 casein can cause leaky gut. Being structurally similar to your thyroid cells, when they get into the bloodstream undigested through your permeable gut lining, these proteins can then become involved in the molecular mimicry process I detailed earlier, where your confused immune system attacks both the proteins and your thyroid tissue.

By removing gluten and dairy from your diet you can help to heal your leaky gut and lower the autoimmune attack on your thyroid tissue.

Identify and eradicate gut infections

Blastocystis hominis and SIBO (small intestinal bacterial overgrowth) are both examples of common gut infections that can cause intestinal permeability.

You can ask a naturopath or GP to order a gut microbiome mapping test and SIBO test to see if you have any bacterial, viral, fungal, or parasitic infections.

If you do, your health practitioner will be best placed to help you eradicate your infection with a combination of dietary and lifestyle modifications as well as herbal and nutritional medicine and/or pharmaceutical medication.

Balance your gut microbiome

Dysbiosis (an imbalance between good and bad bacteria) can cause intestinal permeability. Certain bacteria can also release toxins that can get through the damaged gut barrier into the bloodstream where they trigger antibody attack on the thyroid tissue.

Increasing your intake of probiotic foods such as non-dairy yoghurt and kefir can help to restore gut microbiome balance.

Prebiotic and probiotic supplements can also help to balance the gut microbiome. For autoimmunity, I prescribe my clients the specific probiotic strains Lactobacillus rhamnosus (LGG) and Lactobacillus paracasei (LP-3) as they have been clinically proven to assist in both the prevention of and reduction in severity of autoimmune conditions.

Bowl of yoghurt

Correct nutrient deficiencies

Zinc helps to repair the tight junctions of the intestinal barrier in leaky gut. A safe daily dose of zinc is 25–50mg daily with food, as zinc on an empty stomach can cause nausea. It is essential to check all of the supplements you are taking to ensure you are not having a total dose of more than 50mg daily.

The Therapeutic Goods Administration (TGA) recommends that zinc not be taken in high dosages long term, so it is best to seek the guidance of a naturopath or pharmacist about safe zinc supplementation duration.

Lastly, check if there is Vitamin B6 in your zinc supplement. The TGA has recently lowered the recommended daily dose of Vitamin B6 from 200mg to 100mg due to an increase in reported cases of peripheral neuropathy from Vitamin B6 supplementation. Vitamin B6 is often added to zinc supplements, so make sure you check your zinc formula plus all other supplements you are taking to ensure you are not having a total dose of more than 100mg daily.

Consider supplementation

Supplements such as L-glutamine, collagen peptides, and curcumin can all help to repair intestinal permeability. However, all of these supplements can have potential drug/herb/nutrient interactions and contraindications with certain health conditions, so it is recommended to seek the guidance of a naturopath or pharmacist before supplementing. Your health practitioner can also recommend safe supplementation dosage and duration.

By being proactive in treating the cause of your low thyroid function, Hashimoto’s thyroiditis, you can help to slow down the progression of your autoimmune condition, lessening your symptoms so you can finally feel well.


Tara Ross, Perth women’s hormone health naturopath, sitting at desk with laptop, note book and cup of tea

want to find out how i treat thyroid autoimmunity?

As a naturopath, I can develop a personalised treatment plan for you to treat autoimmunity, a common cause of thyroid conditions, to help you feel energised, shift weight, and think clearly. Take a look at my Thyroid service page for more info…


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