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A Functional Medicine Hypothyroidism Protocol: Comprehensive Testing, Supplements, and Integrative Nutrition

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A Functional Medicine Hypothyroidism Protocol: Comprehensive Testing, Supplements, and Integrative Nutrition

Are your patients experiencing weight gain, fatigue, poor concentration, and depression? It may be time to check their thyroid function. Hypothyroidism, or underactive thyroid, is a common reason for experiencing these symptoms. It affects nearly 5% of Americans over age 12, with a further estimated 5% going undiagnosed. (1)

Conventional treatment of hypothyroidism focuses on thyroid hormone replacement. While this can be an important aspect of treatment, many patients seek a more holistic and integrative approach to management. The art of treating hypothyroidism lies in understanding the complexity of the hormonal feedback axis, the nutritional needs of the thyroid gland, and the underlying causes of thyroid hormone disruption. This article will discuss considerations practitioners should take when diagnosing and managing hypothyroidism and provide a sample integrative treatment protocol that can be implemented in clinical practice.


What is Hypothyroidism?

The thyroid is a butterfly-shaped gland in the front of the neck responsible for synthesizing thyroid hormones. Hypothyroidism, or underactive thyroid, is when the thyroid gland does not produce enough thyroid hormone to meet the body's metabolic needs.

The hypothalamic-pituitary-thyroid (HPT) axis is a feedback loop that controls thyroid function. Thyrotropin-releasing hormone (TRH) is secreted by the hypothalamus in the brain when low thyroid hormones are detected in circulation. TRH signals the brain's pituitary gland to secrete thyroid stimulating hormone (TSH), which travels to the thyroid gland and triggers the release of thyroid hormones thyroxine (T4) and triiodothyronine (T3) by thyroid follicle cells. (2)

Hypothyroidism occurs when there is an interruption at some point along the HPT axis, interrupting normal hormonal signaling and resulting in low circulating thyroid hormones. Primary hypothyroidism occurs due to pathology within the thyroid gland. Secondary hypothyroidism occurs due to insufficient production of TSH by the pituitary gland. Tertiary hypothyroidism is rare but can occur when the hypothalamus fails to release enough TRH. (3, 4)

Subclinical hypothyroidism is a precursor to overt hypothyroidism; it is diagnosed when serum TSH is elevated, but serum T4 is normal.

Symptoms of Hypothyroidism

Symptoms of hypothyroidism often depend on the severity of the condition and develop slowly as the disease progresses and the thyroid produces fewer hormones. The symptoms of hypothyroidism can be attributed to a slowed metabolism. Because every cell in the body requires thyroid hormones to function, they can be present in every body system. (5)

Classic hypothyroid symptoms include:

What Causes Hypothyroidism?

There are multiple reasons why hypothyroidism may occur. In general, risk factors for hypothyroidism include (6):

Hashimoto's thyroiditis is the most common type of hypothyroidism in the United States. This is an autoimmune form of underactive thyroid caused by the body's production of autoantibodies to thyroid peroxidase (TPO) and/or thyroglobulin (TG). These antibodies attack the thyroid gland, causing inflammation and damage within the gland and decreasing thyroid hormone output.

Other causes of hypothyroidism may include thyroid inflammation secondary to infection or radiation, congenital hypothyroidism, surgical removal of the thyroid gland, drug-induced hypothyroidism, and iodine deficiency or excess.

Chronic stress and nutrient deficiencies (e.g., iron, selenium, vitamins A and D, and zinc) can also suppress TSH secretion and impair thyroid hormone synthesis pathways, contributing to subclinical and overt hypothyroidism.

Functional Medicine Labs to Test for Root Cause of Hypothyroidism

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

Complete Thyroid Panel

Conventional doctors typically screen and monitor thyroid function with TSH and free T4. It has been shown that ordering only TSH can miss about 7% of patients with overt thyroid dysfunction. Ordering a complete thyroid panel includes measurement of TSH, total T4 and T3, free T4 and T3, reverse T3, and thyroid antibodies. This thoroughly evaluates the HPT axis, allowing interpreting providers to pinpoint the location and mechanism of HPT dysfunction.

Micronutrient Panel

A specialty micronutrient panel measures extracellular and intracellular levels of essential vitamins, minerals, antioxidants, fatty acids, and amino acids. Knowing extracellular and intracellular micronutrient levels is important in understanding how a patient meets nutritional needs through diet/supplements and how those nutrients function at a cellular level. Deficiencies in tyrosine, iodine, selenium, magnesium, iron, zinc, B vitamins, and vitamins A, E, and D can impair thyroid hormone synthesis and conversion.

Liver Panel

The liver plays a role in thyroid physiology by converting T4 into biologically active T3 and metabolizing excess/used hormones for elimination from the body. A liver panel (hepatic function panel) can screen for and diagnose liver dysfunction, inflammation, and disease possibly contributing to a hypothyroid state.

Gut Assessment

Imbalances in gut health and function can contribute to nutrient malabsorption, systemic inflammation, and thyroid autoimmunity. Especially in patients with concurrent gastrointestinal symptoms, a comprehensive gut assessment, including a SIBO breath test, stool analysis, and gluten sensitivity screening, can reveal triggers of underactive thyroid.

Salivary Cortisol

The adrenal glands secrete cortisol, often called the master stress hormone. Dysfunction of the hypothalamic-pituitary-adrenal (HPA) axis, commonly caused by chronic stress, can influence thyroid function indirectly by cortisol's influences over the HPT axis. A series of salivary cortisol measurements can be used to assess the effects of stress on thyroid function.


Other Lab Tests to Order

Additional labs to consider, based on the needs and symptoms of your patient, include a complete blood count (CBC), lipid panel, and thyroid ultrasound. A CBC will indicate signs of infection contributing to thyroid inflammation and anemias due to nutrient deficiencies. A lipid panel screens for hypercholesterolemia as a consequence of low thyroid. Finally, a thyroid ultrasound images the thyroid and can show signs of inflammation and nodules within the thyroid gland. It is recommended to order an ultrasound if pain, swelling, or enlargement of the thyroid is noticed on a physical exam.

Conventional Treatment for Hypothyroidism

Levothyroxine, replacement T4, is the conventional mainstay for treating hypothyroidism. Starting at a dose of 1.5-1.8 mcg/kg body weight per day, the dose should be increased as needed until the patient experiences symptom relief and TSH normalization. Triiodothyronine, replacement T3, is also available but not typically recommended as a conventional first-line treatment. (7)

Desiccated thyroid extract, derived from porcine thyroid glands, is considered a more "natural" prescription option for thyroid replacement. Containing both T4 and T3,  Armour Thyroid™ and Nature-Throid™ may be preferred by patients seeking integrative medical care. (8)

Regardless of the preparation of thyroid replacement therapy, thyroid hormones should be taken 30-60 minutes before eating and four hours before or after drugs that impede absorption, which include: bile acid sequestrants, calcium carbonate, ferrous sulfate, antacids, proton pump inhibitors, simethicone, and sucralfate. (7)

Functional Medicine Treatment Protocol for Hypothyroidism

The following treatment protocol can be applied to any case of hypothyroidism but is not specific to Hashimoto's thyroiditis. A future article will discuss special considerations when treating Hashimoto's hypothyroidism.

It is important to note and recognize that conventional thyroid replacement may be required in a functional medicine treatment protocol. Prescription thyroid hormones effectively normalize thyroid function, reduce thyroid inflammation, and prevent health complications associated with untreated hypothyroidism.

Nutritional therapy and natural dietary supplements can be safely incorporated into any hypothyroidism protocol to support thyroid function and address underlying causes of thyroid dysfunction identified with specialty lab tests. Protocols should be personalized to the patient's needs and lab results, but a sample protocol can be viewed below.

Nutrition Considerations for Hypothyroidism

A nutrient-rich, anti-inflammatory diet tailored to an individual's food sensitivities can ensure the patient meets the thyroid's nutrient needs and maintains low levels of inflammation within the gastrointestinal tract and thyroid. An anti-inflammatory diet favors high intakes of fruits, vegetables, omega-3 fatty acids, whole grains, lean proteins, and spices while limiting the intake of processed foods, refined sugars, and alcohol. The Mediterranean diet is a well-researched anti-inflammatory diet that has been shown to prevent thyroid diseases.

Eating to support a healthy gut microbiome can also prevent dysbiosis-associated gut inflammation and intestinal permeability. Adding prebiotic- and probiotic-rich foods, including artichokes, garlic, legumes, sauerkraut, and kimchi, feed the healthy bacteria living within the large intestine.

Supplements Protocol for Hypothyroidism

Below are commonly recommended nutritional and herbal supplements suggested by functional medicine providers when treating hypothyroidism.

Thyroid Synergy™

Thyroid Synergy™ by Designs for Health is an all-in-one nutritional support formula for thyroid function. Ingredients include vitamin A, riboflavin, iodine, zinc, selenium, copper, manganese, chromium, tyrosine, American ginseng, and forskolin. The micronutrients provide the body with the building blocks and cofactors required for thyroid hormone synthesis and conversion. Forskolin activates adenylate cyclase within thyroid tissues, stimulating the release of T4 and T3. Adaptogenic ginseng acts on the adrenal glands to help the body adapt to stress and maintain a healthy cortisol level.

Dose: two capsules once daily

Duration: at least 8 weeks

Vitamin D

Vitamin D deficiency is more common in patients with overt and subclinical hypothyroidism than those with normal thyroid function. Vitamin D supplementation in treating hypothyroidism has been associated with improved TSH and thyroid antibody levels.

The dose should be determined based on the patient's vitamin D status. Average doses range from 2,000-5,000 IU once daily.

Duration: at least 12 weeks


Ashwagandha is another adaptogenic herb traditionally used to treat stress and inflammation. Research supports its use in improving markers of physical performance, such as reduced muscle fatigue, tiredness, and pain, and enhancing sleep quality. Preliminary research has also shown that supplementation in patients with hypothyroidism improves serum TSH, T3, and T4 levels. These results indicate that ashwagandha not only can be beneficial in mitigating the symptoms of hypothyroidism but also in improving thyroid function.

Dose: 600 mg once daily

Duration: 8 weeks

When to Retest Labs

Patients often report symptom improvement within two weeks of starting a hypothyroid treatment protocol. Because it can take 6-8 weeks for TSH levels to normalize, it is not recommended to repeat patient labs before this timeframe. Once thyroid hormones are stable, labs can be remeasured every 6-12 months as long as the patient is stable and there is no change to the treatment plan. Any change to the treatment plan should prompt a repeat TSH (at minimum) 6-8 weeks later.



Hypothyroidism is a state of underactive thyroid with various causes. Low thyroid function presents as elevated TSH and low T4 and T3 on labs and commonly leads to many physical symptoms that interfere with quality of life and productivity. Conventional medicine can succeed at restoring a healthy level of thyroid hormone in circulation, but it doesn't address the root cause of endocrine dysfunction. Working with a functional medicine doctor, you can begin to uncover and correct factors impairing thyroid function with specialty labs, nutritional therapy, and dietary and herbal supplements. A functional medicine protocol allows the thyroid to heal to prevent irreversible glandular damage and restore thyroid function to normal.

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


1. Chiovato, L., Magri, F., & Carlé, A. (2019). Hypothyroidism in Context: Where We've Been and Where We're Going. Advances in Therapy, 36(Suppl 2), 47–58.

2. Sweetnich, J. (2023, March 6). The Ultimate Guide to Hypothyroidism Lab Testing. Rupa Health.

3. Nygaard, B. (2010). Hypothyroidism (primary). BMJ Clinical Evidence, 2010.

4. Gupta, V., & Lee, M. (2011). Central hypothyroidism. Indian Journal of Endocrinology and Metabolism, 15(6), 99.

5. Mayo Clinic. (2020). Hypothyroidism (underactive thyroid). Mayo Clinic.

6. Hypothyroidism (Underactive Thyroid) | NIDDK. (2021, March). National Institute of Diabetes and Digestive and Kidney Diseases.

7. Wilson, S.A., Stem, L.A., & Bruehlman, R.D. (2021). Hypothyroidism: Diagnosis and Treatment. American Family Physician, 103(10), 605–613.

8. American Thyroid Association. (2013). Desiccated thyroid extract vs Levothyroxine in the treatment of hypothyroidism. Clinical Thyroidology, 6(8).

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