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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 another estimated 5% going undiagnosed (5). 

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. 


What Is Hypothyroidism?

Hypothyroidism, or underactive thyroid, happens when the thyroid gland produces insufficient thyroid hormone.

The thyroid gland is a butterfly-shaped endocrine gland located in the neck. Thyroid hormones thyroxine (T4) and triiodothyronine (T3) control metabolism, growth, and many other bodily functions by binding their receptors in cells of every organ system in the body. The effects of thyroid hormone are observed in the heart, nervous system, bones, muscles, gastrointestinal tract, immune system, and reproductive organs. (13)

Hypothyroidism Signs & Symptoms

When thyroid hormone levels are too low, metabolism slows, and the following symptoms can occur as a result (13, 37):

  • Fatigue
  • Brain fog
  • Unintentional weight gain
  • Cold intolerance
  • Dry skin and brittle nails
  • Hair loss
  • Constipation
  • Muscle and joint pain
  • Irregular menstrual cycles and heavy periods
  • Insomnia
  • Depression

Root Causes of Hypothyroidism

There are many reasons why hypothyroidism may occur. Uncovering the root cause helps patients and their providers create effective treatment plans that correct obstacles to cure, prevent damage to the thyroid gland, and restore thyroid function.


In iodine-sufficient countries like the United States, Hashimoto's thyroiditis is the most common type of hypothyroidism in the United States. This is an autoimmune condition where the body produces proteins called autoantibodies that attack thyroid peroxidase (TPO) and/or thyroglobulin (TG). This inflames and damages the thyroid gland, decreasing thyroid hormone output. 

Some main factors contributing to autoimmunity include genetics, intestinal dysbiosis and hyperpermeability, emotional stress, infection, exposure to environmental toxins, and hormonal imbalances.

Nutrient Deficiencies

Globally, iodine deficiency is the most common cause of hypothyroidism. Iodine is a trace mineral the thyroid gland needs to make thyroid hormones. In the United States, iodine deficiency is extremely rare, and excess iodine intake can trigger thyroid autoimmunity and hypothyroidism.

The body also requires other vitamins and minerals to make and convert thyroid hormones efficiently. Magnesium, vitamin B12, and vitamin D deficiencies have been associated with hypothyroidism. Research shows that iron, selenium, and zinc supplementation leads to improved outcomes in patients with hypothyroidism. (14

Medical Treatments

Some people with thyroid nodules, thyroid cancer, or Graves' disease (an autoimmune form of hyperactive thyroid) may require surgical removal or radiation to the thyroid gland, which can result in hypothyroidism.

Certain medications can interfere with normal thyroid signaling, induce thyroid autoimmunity, or trigger inflammation within the gland, leading to drug-induced hypothyroidism.

Congenital Hypothyroidism

Congenital hypothyroidism (thyroid hormone deficiency at birth) affects one out of 3,000 to 4,000 live births. It primarily occurs due to abnormal thyroid development in utero. (2


Thyroiditis refers to inflammation within the thyroid gland that, if not addressed, can lead to reduced thyroid function over time. Common causes of thyroiditis include autoimmunity, viral infection, and hormonal fluctuations associated with the postpartum period.

Damage to the Pituitary Gland

The pituitary gland (located in the brain) tells the thyroid how much hormone to make by producing thyroid-stimulating hormone (TSH). Pituitary damage from a tumor, surgery, or elevated intracranial pressure can result in insufficient TSH and secondary hypothyroidism.

How to Diagnose Hypothyroidism

When a patient's medical history, clinical symptoms, and physical exam findings raise suspicion of hypothyroidism, a definitive diagnosis should be made by ordering a thyroid panel.

Step 1: Measure Thyroid Hormones

TSH, free T4, and free T3 are the main blood tests ordered to assess thyroid function and measure thyroid hormones. An elevated TSH with low free T4 and/or T3 is diagnostic for hypothyroidism, while an elevated TSH with normal T4 and T3 levels indicates subclinical hypothyroidism.

These are thyroid panels that doctors can order: 

Step 2: Test for Hashimoto's Thyroiditis

Because Hashimoto's thyroiditis is the most common form of hypothyroidism in the United States, many doctors will order thyroid antibodies (anti-TPO and anti-TG) at the same time as ordering thyroid hormones. Elevations in either or both antibodies confirm a diagnosis of Hashimoto's.

Thyroid antibodies can be ordered individually or as part of a comprehensive thyroid panel: 

Step 3: Thyroid Ultrasound

Sometimes, your doctor may recommend a thyroid ultrasound as part of the initial diagnostic evaluation for hypothyroidism. A thyroid ultrasound is usually ordered if a doctor finds any of these findings during physical exam: 

  • Thyroid nodule
  • Thyroid goiter
  • Enlarged cervical lymph nodes

Step 4: Order Additional Testing to Uncover Root Causes of Thyroid Dysfunction

Other tests can help provide insight into the underlying reason behind hypothyroidism.

Comprehensive Stool Analysis (CSA)

Leaky gut, intestinal inflammation, and dysbiosis can impair the optimal absorption of thyroid-essential nutrients and trigger autoimmunity. A CSA analyzes various fecal biomarkers to screen for these possible hypothyroid triggers. 

The following tests are examples of popular CSAs: 


Micronutrient testing measures the levels of essential vitamins, minerals, and other micronutrients in an individual's body to provide insight into nutritional imbalances that can impair thyroid function.

These are micronutrient testing options: 

Comprehensive Hormone Testing

Because hormonal imbalances can contribute to the development of thyroid autoimmunity and thyroiditis, hormone testing may be warranted, especially for patients with symptoms like irregular periods, hot flashes, infertility, low libido, and mood swings. 

The following comprehensive hormone panels are an excellent place to start: 


Treatment Plan for Hypothyroidism

Below is a step-by-step treatment plan that can be personalized for patients struggling with hypothyroidism.

1. Replace Thyroid Hormones

Here's Why This Is Important: 

Untreated hypothyroidism can lead to potentially severe health consequences. Thyroid hormone replacement brings thyroid hormones into a normal range to prevent these complications, in addition to quickly alleviating hypothyroid symptoms.

How Do You Do This?

Thyroid replacement with levothyroxine (synthetic T4) is the standard treatment to restore thyroid hormones to within a normal range. Starting at a dose of 1.5-1.8 mcg/kg body weight per day, the dose should be increased every 6-8 weeks until the patient experiences symptom relief and TSH normalization. (20, 41

Liothyronine is synthetic T3. It is not typically recommended as a first-line treatment but can benefit patients who do not feel completely normal with T4 monotherapy. (20, 41

Porcine-derived desiccated thyroid extract is considered a more "natural" pharmaceutical option for thyroid replacement. It is derived from pig thyroid glands and contains a fixed ratio of T4 and T3 in each dose.

To ensure thyroid hormones are absorbed, they should be taken on an empty stomach around the same time each day. The most popular administration method is taking thyroid hormones in the morning 30-60 minutes before eating breakfast. (19, 41

Certain medications and supplements can interfere with the absorption of thyroid hormone. These should be taken 3-4 hours after taking thyroid hormone (19, 41):

  • Fiber supplements
  • Calcium
  • Iron
  • Multivitamins
  • Proton pump inhibitors
  • Bile acid sequestrants
  • Soy products

2. Correct Nutrient Deficiencies

Here's Why This Is Important:

Nutrient deficiencies can impair the thyroid's natural ability to produce the appropriate amounts of thyroid hormone. Nutrient therapy provides the micronutrient building blocks and cofactors the thyroid needs to synthesize its hormones. 

How Do You Do This?

Deficient nutrients can be normalized to an optimal level through dietary supplementation and maintained with a diverse, healthy diet. 

Research shows that the following dosages of nutrients improve outcomes for patients with hypothyroidism. Supplements should be personalized based on lab results and each patient's needs.

The Mediterranean diet's principles encourage consuming fruits, vegetables, whole grains, healthy fats, and lean proteins that supply adequate amounts of thyroid-essential nutrients, including iodine, selenium, iron, zinc, and vitamins B12, D, and A. These tips can help you get started with a Mediterranean diet: 

  • Eat 2-3 servings of fruit and at least four servings of vegetables daily
  • Substitute refined grains for whole grains. Examples include brown rice, quinoa, oats, farro, and buckwheat.
  • Eat seafood 2-3 times weekly
  • Use olive oil as one of your primary fat sources. 
  • Season your food with anti-inflammatory herbs and spices.

3. Heal the Gut

Here's Why This Is Important:

Poor gut health is correlated to nutrient deficiencies, hormonal imbalances, immune dysfunction, and inflammation. 

How Do You Do This?

A 5-R protocol is a framework used to support and heal the digestive tract:

  • Remove foods, environmental toxins, medications, and other stressors that trigger inflammation
  • Replace digestive enzymes to support healthy digestion and absorption of food
  • Reinoculate the gut with beneficial bacteria through the use of prebiotic and probiotic foods and supplements
  • Repair the gut lining with healing foods (e.g., bone broth) and supplements (e.g., l-glutamine, zinc carnosine, marshmallow root)
  • Rebalance the body to prevent digestive dysfunction by prioritizing healthy lifestyle habits, such as a nutritious diet, regular exercise, good sleep, and stress management.

4. Balance Hormones

Here's Why This Is Important:

The endocrine system comprises various glands and over 50 hormones that interact with one another. An imbalance in one hormone can lead to an imbalance in another. For example, excess estrogen has been implicated in thyroid autoimmunity and hypothyroidism. High cortisol, often caused by chronic stress, can suppress TSH and eliminate the thyroid's signal to produce thyroid hormones. 

How Do You Do This? 

Make mindful dietary choices that support detoxification pathways. Specifically: 

  • Eat fiber- and phytonutrient-rich foods like nuts, seeds, whole grains, leafy green vegetables, and berries.
  • Incorporate cruciferous vegetables, such as Brussels sprouts, broccoli, and kale, which are rich in diindolylmethane (DIM), which supports liver health and estrogen metabolism.
  • Avoid ultra-processed foods and refined sugars. 

Get the recommended amount of sleep based on your age. Adults should sleep 7-9 hours every night.

Manage stress healthfully by fostering healthy relationships, practicing mind-body medicine, and exercising regularly. 

5. Follow Up

Here's Why This Is Important:

Routine thyroid testing ensures that thyroid hormones remain within the optimal range for proper bodily function. Monitoring thyroid hormone levels helps evaluate the efficacy of the current treatment plan, ensuring that the prescribed medications effectively restore hormone balance. If not, abnormal results prompt timely treatment modifications.

How Do You Do This? 

A repeat thyroid panel should be checked 6-10 weeks after initiating or modifying a pharmaceutical protocol. Once thyroid hormones are optimized, labs can be remeasured every 6-12 months as long as the patient is stable and the treatment plan does not change. (30

The Risks of Untreated Hypothyroidism

Left untreated, hypothyroidism can lead to myxedema coma, a life-threatening condition that requires emergency medical treatment. Its symptoms include intense cold intolerance, extreme lack of energy, and loss of consciousness.

Hypothyroidism can also increase the risk of developing:

  • Thyroid enlargement (goiter), which can cause problems with swallowing and breathing
  • High cholesterol, which increases the risk of heart disease
  • Peripheral nerve damage
  • Infertility
  • Physical and mental developmental problems in untreated babies born with congenital hypothyroidism  
  • Babies born to people with untreated hypothyroidism have an increased risk of being born with birth defects

Hypothyroidism Case Study

You can read about an actual hypothyroid-related case study here: 

Tinnitus Due to Hypothyroidism: How Lauren's Doctor Connected the Dots: A Case Study


Key Takeaways:

  • Hypothyroidism is a common medical condition characterized by an underactive thyroid gland. Because thyroid hormones are required by every cell in the body to fuel metabolism, the effects of hypothyroidism are profound and systemic. 
  • Hypothyroidism can't always be cured, but it can be well-managed with thyroid hormone replacement. 
  • A holistic treatment plan encourages patients to correct underlying imbalances contributing to thyroid dysfunction. Treatment goals include reducing thyroid inflammation, preventing thyroid damage, and optimizing thyroid function. In some cases, it is possible to enhance thyroid function naturally and decrease the body's requirement for hormone replacement.
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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