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A Functional Medicine Hashimoto Treatment Protocol: Testing, Supplements, and Nutrition

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A Functional Medicine Hashimoto Treatment Protocol: Testing, Supplements, and Nutrition

The thyroid is a butterfly-shaped endocrine gland in the neck responsible for producing and releasing thyroid hormones into the bloodstream. Thyroid hormones thyroxine (T4) and triiodothyronine (T3) are responsible for regulating many metabolic and essential bodily functions, including cardiovascular function, body temperature, body weight, nervous system function, digestion, growth and development, menstruation, muscle contractions, breathing, and waste elimination. (1)

Hashimoto's thyroiditis is an autoimmune disease that negatively affects thyroid function. In developed countries, it is the most common cause of hypothyroidism and is estimated to affect 5% of Americans. Women are 4-10 times more likely to develop Hashimoto's disease than men, especially between the ages of 30-50. (2)  

Hypothyroidism is most commonly diagnosed when a screening serum thyroid stimulating hormone (TSH) comes back elevated. However, an annual screening of TSH is estimated to miss 7% of hypothyroid cases. Additionally, thyroid autoantibodies are detectable in patients up to years before clinical signs and symptoms appear. Advanced screening methods and integrative approaches allow functional medicine providers to intervene in the early stages of Hashimoto's thyroiditis and target root causes of autoimmunity to achieve better health outcomes.


What is Hashimoto's Disease?

Hashimoto's disease (also called chronic lymphocytic thyroiditis and autoimmune thyroiditis) is an autoimmune form of hypothyroidism that accounts for 90% of adult hypothyroidism. Autoimmunity occurs when the body's immune system produces autoantibodies to self-tissues, causing tissue inflammation and destruction. In Hashimoto's thyroiditis, antibodies formed against thyroglobulin (TG) and thyroid peroxidase (TPO) impair the thyroid's ability to produce hormones and can cause permanent thyroid damage over time.

Hashimoto's Disease Symptoms

The initial stages of Hashimoto's can destroy thyroid cells and cause an increased release of thyroid hormone into the bloodstream, presenting as hyperthyroidism with symptoms like increased appetite, sweating, heart palpitations, diarrhea, insomnia, and anxiety.

However, after this period of destruction, due to impaired thyroid capacity, insidious signs and symptoms of hypothyroidism will appear, affecting nearly every organ system in the body, including (3):

  • Dry, thinning hair and skin
  • Brittle nails
  • Loss of the outer third of eyebrows
  • Puffy face
  • Enlarged thyroid
  • Slow heartbeat
  • Muscle and joint pain
  • Weight gain
  • Constipation
  • Cold intolerance
  • Depression
  • Fatigue
  • Forgetfulness
  • Menstrual disorders
  • Infertility

Untreated hypothyroidism can result in chronic health complications like heart disease, heart failure, hypertension, and high cholesterol. Myxedema is a life-threatening condition caused by chronically untreated hypothyroidism that occurs when the body's vital processes slow down, presenting as profound lethargy and unconsciousness. (3)

What Causes Hashimoto's Disease?

All autoimmune diseases are known to be multifactorial, arising from the interplay of environmental factors in genetically predisposed individuals, causing immune dysfunction, loss of self-tolerance, and the production of autoantibodies.

Specific triggers known to play a role in the pathogenesis of Hashimoto's include selenium and vitamin D deficiencies, excessive iodine intake, infections, anticancer drugs, stress, intestinal permeability, and environmental toxins. (3-5)

The presence of acute and chronic infections can stimulate autoimmunity through molecular mimicry. This occurs when similarities between foreign and self-proteins favor the activation of autoreactive immune cells and an attack on self-tissues. Infectious pathogens implicated in the development of Hashimoto's include Helicobacter pylori, Yersinia enterocolitica, Candida albicans, Epstein-Barr virus (EBV), and Borrelia burgdorferi. (4, 6)

Exposure to heavy metals and toxic chemicals, such as those in plastics and pesticides, contributes to intestinal dysbiosis, inflammation, and thyroid autoimmunity by disrupting normal detoxification and endocrine pathways. (4)

Functional Medicine Labs to Test for Root Cause of Hashimoto's Disease

Ordering and interpreting a comprehensive panel of specialty tests, and comparing a patient's results to optimal reference ranges, supports the early diagnosis of autoimmune thyroid disease and the identification of underlying causes contributing to thyroid dysfunction.

Thyroid Panel

A complete thyroid panel, including TSH, free T3 and T4, total T3 and T4, reverse T3, and thyroid antibodies (anti-TPO and anti-TG), is essential in diagnosing autoimmune thyroid disease. Ordering the above thyroid biomarkers ensures a comprehensive evaluation of thyroid hormone synthesis, conversion, and autoimmunity to diagnose early thyroid dysfunction and understand the pathological mechanism(s) behind it. Elevated TSH, low T4 and T3 values, and elevated anti-TPO and/or anti-TG are diagnostic for Hashimoto's thyroiditis.

Standard reference ranges help detect overt thyroid disease; however, as discussed above, thyroid autoimmunity can occur in the background for years before overt Hashimoto's thyroiditis is seen on standard labs. In addition, many patients will experience hypothyroidism symptoms despite their labs returning as "normal" based on standard reference ranges. Evaluating the thyroid panel using optimal/functional reference ranges inspires precision and detection of thyroid dysfunction so that early interventions can be implemented to prevent disease progression and irreversible thyroid damage. (7)

Food Sensitivities

Unidentified food sensitivities contribute to increased intestinal permeability, systemic inflammation, and the formation of autoimmune responses. Food sensitivities often cause vague and delayed reactions and, because of this, can be challenging to identify without specialty testing. Food sensitivity testing can help pinpoint specific food-related triggers associated with an individual's Hashimoto's disease so that dietary modifications can be personalized to their needs.

Gluten is highly involved in thyroid autoimmunity because of its similar appearance to an enzyme called transglutaminase in the thyroid gland. The evidence overwhelmingly suggests the interconnection between gluten intolerance and thyroid autoimmunity. A blood panel can help screen for celiac disease and gluten sensitivity, which can significantly contribute to the severity of thyroid disease.


The Pathogen-Associated Immune Reactivity Screen (Array 12) by Cryex Laboratories is a broad all-in-one infectious screening to rule out active, chronic, and latent infections that increase susceptibility to autoimmune diseases.

Environmental Toxins

Combining urinary tests to screen for heavy metals and chemicals can help identify toxin exposure when the patient's history does not obviously identify the causative agent. These panels identify toxic agents contributing to disease and provide a picture of how well the patient's detoxification pathways are functioning.

Functional Medicine Labs to Test That Can Help Individualize Treatment of Hashimoto's Disease

Functional medicine labs help practitioners personalize treatment options for their patients. Below are some of the most common labs ordered for patients suffering from Hashimoto's thyroiditis.

Cardiometabolic Assessment

Hypothyroidism can lead to high cholesterol, dysglycemia, and liver dysfunction. A comprehensive metabolic panel (CMP) and lipid panel can be used to screen for cardiovascular and hepatic inflammation resulting from low thyroid levels that can further exacerbate thyroid autoimmunity.

Comprehensive Stool Test

The gut-thyroid axis refers to the intimate bidirectional communications between the intestinal microbiome and the thyroid through the metabolic actions of beneficial gut microbes. A comprehensive stool analysis assesses digestive function, intestinal inflammation, and the intestinal microbiome to screen for infection, dysbiosis, and other gastrointestinal factors that impact the gut-thyroid axis.

Comprehensive Hormone Panel

Acute and chronic stress cause changes in cortisol secretion, which can interfere with the thyroid axis, resulting in poor thyroid hormone synthesis, secretion, and conversion. Stress and hypothyroidism, together and independently, can cause menstrual cycle irregularities and other hormonal symptoms. A comprehensive hormone panel measures cortisol and sex hormone metabolites for a holistic evaluation of the endocrine system.

Micronutrient Panel

Nutrient imbalances can lead to thyroid impairment, inflammation, and immune dysregulation. A nutritional assessment measures intra- and extracellular levels of essential vitamins, minerals, antioxidants, amino acids, and fatty acids. These results can be used to target therapies to meet specific nutritional and clinical goals.


Conventional Treatment for Hashimoto's Disease

The conventional algorithm for treating Hashimoto's disease relies on levothyroxine, replacement T4, to bring TSH back into the normal reference range. Other thyroid replacement medications, such as liothyronine (replacement T3) and desiccated thyroid preparations, are not emphasized in conventional medical approaches.

Functional Medicine Treatment Protocol for Hashimoto's Disease

A functional medicine treatment approach to Hashimoto's disease differs from its conventional counterpart by putting weight on addressing autoimmunity as the root cause of hypothyroidism. While thyroid replacement is often indicated for patients to normalize thyroid hormones and provide symptomatic relief, an integrative medicine treatment plan also incorporates natural modalities to treat the patient holistically and improve clinical outcomes.

Therapeutic Diet and Nutrition Considerations for Hashimoto's Disease

A nutrient-dense anti-inflammatory diet, such as the autoimmune protocol (AIP) diet, should be tailored to the patient's dietary preferences and sensitivities. A referral to a functional nutritionist may be indicated because making nutritional modifications while meeting sufficient caloric and nutrient needs can be challenging.

Those with concurrent celiac disease or gluten sensitivity should remove gluten from the diet; studies positively associate a gluten-free diet with reductions in thyroid autoantibodies.

Research strongly supports the correlation between iodine intake with increased thyroid antibody titers. Studies demonstrate that daily iodine restriction to less than 100 mcg normalizes thyroid function and incites a return to a euthyroid state. Processed foods with iodized salt, seaweed, dairy, and dietary supplements are typical sources of excessive iodine intake. (8-10)

Supplements Protocol for Hashimoto's Disease

Dietary supplements can supplement dietary interventions, lifestyle modifications, and other complementary and integrative medicinal modalities to improve factors associated with autoimmunity and an underactive thyroid.


Myo-inositol is an endogenous sugar the body makes that is important in hormonal signaling. It regulates iodine oxidation needed to produce thyroid hormones and combats excessive oxidative stress and inflammation to protect thyroid cells. Supplementation of Myo-inositol results in reduced TSH, thyroid antibodies, and thyroid size (16, 17).

Dose: 600 mg daily

Duration: at least six months


Selenium is an antioxidative trace mineral that plays a major role in supporting metabolism, the immune system, and thyroid function. Selenium supplementation in patients with Hashimoto's results in decreased TPO antibodies by up to 63.6%, normalization of thyroid hormones, and improvement in hypothyroid symptoms. (11-13)

Dose: 200 mcg daily

Duration: at least three months


Glutathione is often referred to as the body's master antioxidant. Glutathione diminution is a hallmark characteristic of oxidative stress and the development of immunological production of thyroid antibodies leading to Hashimoto's disease. Glutathione can be taken orally or applied topically to the thyroid.

Dose: Apply one pump topically to the thyroid three times daily

Duration: at least one month

Vitamin D

Vitamin D deficiency states are correlated with exaggerated inflammatory reactions and thyroid autoimmune diseases like Hashimoto's. One study found that 85.3% of Hashimoto's patients were deficient in vitamin D and that supplementation restored vitamin D status and decreased anti-TPO by 20.3%. Numerous studies demonstrate that vitamin D significantly improves self-tolerance and modulates inflammation, as shown by the inverse relationship between 25-hydroxyvitamin D levels and thyroid antibody titers. (14, 15)

Dose: 2,000 IU daily

Duration: at least six months

When to Retest Labs

It is recommended that, at minimum, TSH be remeasured 6-8 weeks after changing a patient's medications and/or supplements to assess thyroid status accurately. Note that changes to thyroid antibodies may take up to three months to measure on labs. Once the patient reaches a euthyroid state, lab monitoring frequency can be reduced to every 6-12 months.



Given the thyroid's far-reaching effects on the body, managing Hashimoto's hypothyroidism can quickly become complex. A functional medicine approach to Hashimoto's disease appreciates the "Hashimoto's Web" - the notion that autoimmunity and underactive thyroid are not limited to the thyroid and, instead, cause whole-body disease. The impacts of hypothyroidism on every body system perpetuate autoimmunity, creating a vicious cycle of systemic inflammation and dysregulation. The functional medicine doctor's role is to untangle this web delicately; and, in doing so with an integrative approach, can restore balance, health, and well-being to the Hashimoto's patient.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

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11. Feldt, M. (2021, April 13). Hormonal Health – Thyroid Support. Fullscript.

12. Toulis, K.A., Anastasilakis, A.D., Tzellos, T.G., et al. (2010). Selenium Supplementation in the Treatment of Hashimoto's Thyroiditis: A Systematic Review and a Meta-analysis. Thyroid, 20(10), 1163–1173.

13. Wichman, J., Winther, K.H., Bonnema, S.J., et al. (2016). Selenium Supplementation Significantly Reduces Thyroid Autoantibody Levels in Patients with Chronic Autoimmune Thyroiditis: A Systematic Review and Meta-Analysis. Thyroid, 26(12), 1681–1692.

14. Mazokopakis, E.E., Papadomanolaki, M.G., Tsekouras, K.C., et al. (2015). Is vitamin D related to pathogenesis and treatment of Hashimoto's thyroiditis? Hellenic Journal of Nuclear Medicine, 18(3), 222–227.

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