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Fatigue, Weight Gain, Depression, And Brain Fog Are Common Signs Of This Autoimmune Disease

Medically reviewed by 
Fatigue, Weight Gain, Depression, And Brain Fog Are Common Signs Of This Autoimmune Disease

The thyroid is the butterfly-shaped gland at the base of the neck. Hormones produced by the thyroid are essential for regulating metabolism, body temperature, energy, heart rate, menstrual cycle, mood, and hair and nail growth.

Hashimoto’s disease (chronic lymphocytic thyroiditis or autoimmune thyroiditis) is an autoimmune condition where the body produces antibodies that attack and damage the thyroid. This immune attack impairs the thyroid’s ability to produce hormones over time. Since these hormones impact every cell in the body, Hashimoto’s can have wide-reaching consequences.

Hashimoto’s is the most common cause of hypothyroidism (an underactive thyroid) in iodine-sufficient areas of the world like the US, impacting 1-4% of Americans. Hashimoto’s is ten times more common in women than men, developing most commonly between ages 30 to 50. While Thyroid Stimulating Hormone (TSH) is often used as a screening test, it is not enough alone to fully assess thyroid function.


Hashimoto’s Disease Signs & Symptoms

Over time with this autoimmune condition, the body produces antibodies that attack the thyroid (TPO antibodies). This attack on the thyroid causes inflammation and renders the gland less effective at producing hormones. The resulting decrease in thyroid hormones impacts cells throughout the body, causing symptoms such as:

  • Fatigue
  • Weight gain
  • Headaches and migraines
  • Thinning or dry hair, nails, and skin
  • Feeling cold all the time
  • Irregular periods
  • Puffiness or fluid retention
  • Fertility problems
  • Slow digestion and constipation
  • Brain fog
  • Depression
  • Aching muscles and joints
  • Loss of muscle strength and tone

These symptoms may be vague early on, but the inflammation can result in an enlarged thyroid (goiter) and thyroid nodules over time. Untreated hypothyroidism can also lead to additional bodywide complications, including:

  • Elevated cholesterol
  • Heart disease and heart failure
  • High blood pressure
  • Pregnancy complications
  • Myxedema- a rare, life-threatening condition where the body’s functions slow down significantly.

A Hashimoto’s flare, especially early in the disease process, can cause a hyperthyroid state. As the thyroid comes under attack from autoantibodies, the cells of the gland can release hormones quickly into the bloodstream, leading to symptoms of hyperthyroidism like

  • Fatigue
  • Heat intolerance
  • Irritability
  • Rapid heartbeat
  • Sleep problems
  • Anxiety

Hashimoto’s Disease Possible Causes

Digestive Factors

Various factors underlie autoimmunity that causes Hashimoto’s, including gut health, nutrition, infections, environmental exposures, and genetics. The immune system becomes dysregulated when someone with a genetic predisposition is exposed to environmental or other factors.

The digestive tract is a barrier to the outside world and a critical immune system mediator. The microbiome plays a critical role in regulating hormones, immunity, and detoxification. Ongoing stressors lead to dysbiosis, where bacteria become imbalanced and damage the gut lining, contributing to inflammation. With chronic exposures to toxicants, inflammatory foods such as gluten or lectins, and chronic stress, the barrier becomes ineffective, and substances enter the body and trigger autoimmune responses and inflammation throughout.

A damaged digestive system can lead to imbalances in nutrients like selenium, zinc, tyrosine, and essential fatty acids that regulate the immune system and help balance the thyroid and other hormones.


Viral or bacterial infections such as Helicobacter Pylori and Yersinia enterocolitica can contribute to molecular mimicry where the immune system mistakenly identifies its own tissues as foreign invaders and attacks.


Exposures to heavy metals, mercury, arsenic, plastics, and pesticides contribute to dysbiosis, inflammation, and autoimmunity by harming the body’s detoxification, nervous, and endocrine systems.

Fluoride and bromine in municipal water supplies, flame retardants, and some baked goods compete with iodine in the thyroid gland, impacting its functioning.  

Autoimmune Diseases

Those with other autoimmune disorders such as celiac disease, lupus, rheumatoid arthritis, Sjogren’s syndrome, and type 1 diabetes are more likely to develop Hashimoto’s. Many patients also have a family history of the condition.

Functional Medicine Labs to Test for Hashimoto’s Disease

Functional medicine testing can diagnose Hashimoto’s and identify underlying causes. Testing should assess immune system balance to uncover the causes of autoimmunity and systemic inflammation.

Thyroid Function and Autoantibodies

A Complete Thyroid Panel including thyroid-stimulating hormone (TSH), T3 (free and total), T4 (free and total), and reverse T3 should be assessed using functional medicine ranges.

  • TSH measures how the pituitary gland in the brain communicates with the thyroid, indicating hypothyroidism when elevated. A normal TSH does not rule out thyroid issues on its own since it is an indirect measure of function.
  • Free T4 measures bioavailable unbound thyroid hormone and is a marker of low thyroid function when decreased.
  • In the peripheral tissues, T4 is converted to T3. Low T3 indicates decreased thyroid function or a problem with conversion, which often occurs with chronic stress, inflammation, or high toxic burden.
  • Some T4 is also converted to reverse T3, which serves as a “brake” by competing with free T3 for cell receptors. High reverse T3 can cause hypothyroidism and usually reflects a systemic issue like chronic inflammation.

In addition, testing for thyroid peroxidase (TPO) and anti-thyroglobulin (TG) antibodies help diagnose Hashimoto’s. Elevated TPO antibodies are typical, and thyroglobulin antibodies may also be elevated and are associated with symptom burden.

Thyroid Supportive Nutrients

Nutrients including iodine, iron, tyrosine, zinc, selenium, magnesium, and vitamins E, B2, B3, B6, C, and D all contribute to proper thyroid balance. Other nutrients like vitamin A improve cellular sensitivity to thyroid hormones.

Micronutrient testing analyzes how well your body is absorbing these nutrients.

Gut Health

Since dysbiosis and leaky gut contribute to autoimmunity, assessing gut health helps provide targeted interventions to regain balance. A Comprehensive Stool Test measures amounts of healthy and unbalanced gut bacteria (dysbiosis), inflammatory markers, leaky gut, parasites, and yeast to assess the state of the gut and guide treatment.

Food Sensitivities

Food sensitivities and allergies contribute to intestinal permeability, inflammation, and autoimmunity. ELISA testing identifies foods to which an individual is sensitive.

In particular, a protein within gluten called gliadin is molecularly very similar to transglutaminase in the thyroid. When the gut lining is leaky (which can be worsened by consuming gluten and other foods one is sensitive to), gluten can enter the bloodstream and encounter cells of the immune system. In Hashimoto’s, the immune system is already primed to attack the thyroid tissue, so additional immune stimulation and this molecular mimicry by gluten proteins trigger the body to attack the thyroid further, contributing to worsening symptoms. Testing for gluten sensitivity or celiac disease with Genova Diagnostics Celiac and Gluten Sensitivity and evaluating the leaky gut marker zonulin can help uncover these contributing factors.


Specialized labs assess methylation, detoxification capacity, and glutathione production to understand genetic susceptibilities and current detoxification ability. This type of testing helps pinpoint specific areas to support that can help bring the body back into balance.


Functional Medicine Treatment for Hashimoto’s Disease

While thyroid hormone replacement medication is often part of a comprehensive treatment approach, it does not treat the disease itself but rather the symptoms of low thyroid hormones. A functional medicine approach to treating Hashimoto’s aims to rebalance and regulate the immune system. It is vital to figure out and avoid individual triggers that cause autoimmunity to prevent cumulative damage and thyroid dysfunction. Utilizing lifestyle and functional medicine approaches to address the root cause also supports healing the thyroid.

Individualized Anti-inflammatory Diet

Inflammation increases autoimmunity, so a nutrient-rich, anti-inflammatory diet tailored to individual sensitivities and needs can restore balance.

Individualized Food Sensitivity Elimination Diet

Eliminating trigger foods, such as gluten and grains, dairy, processed sugars, and other foods an individual is sensitive to while balancing the intake of micronutrients like vitamin A, zinc, vitamin D, omega-3 fatty acids, and selenium can reduce inflammation and avoid decreased thyroid function due to nutrient deficiencies.

Note: While the thyroid uses iodine to make hormones, too much iodine intake (often from salt in processed foods or excessive seaweed consumption) can negatively affect function.

Rebalance the Microbiome

Since the microbiome significantly impacts the immune system, maintaining diverse and balanced gut bacteria helps tame autoimmunity.

Restoring gut diversity by eating various whole foods and incorporating probiotic-rich foods like kimchi and sauerkraut and prebiotic-rich foods like artichokes, garlic, and beans will nourish healthy bacteria, which is critical for repairing the mucosal barrier and halting autoimmunity.

Adequate Sleep and Stress Management

Chronic stress contributes to inflammation and is associated with autoimmunity. Finding balance via adequate sleep, stress management, and balanced movement can improve thyroid- and overall health. Restorative exercises such as yoga, walking, and Qi gong balance inflammation more than overly intense exercise. Time in nature also reduces inflammation via exposure to sunlight to optimize vitamin D and direct contact with the earth.

Address Environmental Factors

Chemicals in plastics, pesticides, heavy metals, and other pollutants can disrupt thyroid function. High-quality water and air filters, organic produce, and assessment of other exposures such as metal dental amalgams help reduce exposures.



Since Hashimoto’s is a multisystemic disease, identifying and addressing root causes of inflammation and autoimmunity can halt further damage and allow the thyroid to heal.

A Functional Medicine approach to Hashimoto’s includes screening for a comprehensive thyroid panel, and assessing supportive thyroid nutrients, markers of gut health, food sensitivities, and detoxification capacity.

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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