Hashimoto’s & Thyroid Autoimmunity
Hashimoto’s thyroiditis is an autoimmune disease in which the immune system attacks the thyroid gland, gradually reducing its ability to produce thyroid hormones.
Standard treatment usually involves replacing deficient thyroid hormone with levothyroxine. This works well for many people, but it does not directly target the autoimmune process itself.
Researchers are studying the possible roles of genetics, nutrition, nutrient deficiencies, infections, the gut microbiome, and environmental factors. Some functional-medicine physicians are particularly interested in whether addressing these factors may improve symptoms or influence thyroid autoimmunity.
What Is Hashimoto’s Disease?
Hashimoto’s is the most common cause of hypothyroidism in the United States. The immune system produces antibodies—most commonly thyroid peroxidase (TPO) antibodies—associated with inflammation and damage to the thyroid gland.
As thyroid function declines, symptoms can include fatigue, feeling cold, weight gain, constipation, dry skin, muscle weakness, and difficulty concentrating.
Diagnosis usually includes blood tests measuring TSH and thyroid hormone levels, and sometimes thyroid antibodies. Some people have elevated antibodies while thyroid hormone levels remain normal.
For an explanation of these measurements and what they reveal about thyroid function, see Thyroid Tests — TSH, Free T4 and Free T3.
Conventional Treatment
When Hashimoto’s causes hypothyroidism, standard treatment is levothyroxine, a synthetic form of thyroid hormone T4. The dose is adjusted primarily by monitoring TSH and, when appropriate, free T4.
Alternatives include desiccated thyroid extract such as Armour Thyroid and adding liothyronine (T3) to levothyroxine. Some people report feeling better with these approaches, although studies have not established that they are generally superior. Levothyroxine remains the standard treatment.
Thyroid hormone replacement does not eliminate the autoimmune process that caused the thyroid damage. This has led researchers to investigate whether diet, nutrient status, the gut microbiome, and other environmental factors might influence thyroid autoimmunity.
Diet, Gluten & Hashimoto’s
People with autoimmune thyroid disease are more likely to have celiac disease, and those with both conditions need a strict gluten-free diet.
Whether people with Hashimoto’s without celiac disease benefit from avoiding gluten is less clear. A 2025 systematic review found only three eligible studies involving 110 people and concluded that the evidence was very uncertain, with no clear improvement in TSH, T3, or T4.
Some functional-medicine physicians, including Datis Kharrazian, Mark Hyman, and Susan Blum, recommend experimenting with gluten elimination. Some patients report improvement, but no single diet has been shown to be best for everyone with Hashimoto’s.
Selenium, Vitamin D & Other Nutrients
Selenium is important for normal thyroid function. A 2024 review of 35 studies found that supplementation reduced TPO antibodies and produced a small reduction in TSH among people not taking thyroid hormone. Whether these changes improve symptoms or long-term outcomes remains uncertain, and excess selenium can be harmful.
Vitamin D has also been studied. Trials and meta-analyses suggest supplementation may reduce thyroid antibody levels, particularly in people with low vitamin D, but whether this changes the long-term course of Hashimoto’s is uncertain.
Iodine is essential for thyroid hormone production, but excessive intake can contribute to thyroid dysfunction or autoimmunity in susceptible people.
The important principle is that correcting a deficiency is different from taking large doses of supplements without evidence of need.
The Functional Medicine Approach
Functional medicine asks whether potentially modifiable factors—including diet, nutrient deficiencies, gut health, infections, stress, environmental exposures, and metabolic health—may contribute to symptoms or autoimmune activity.
Datis Kharrazian, Susan Blum, and Mark Hyman have been prominent advocates of this approach. Evidence varies considerably among individual interventions.
For someone interested in exploring these approaches, one reasonable strategy is to make careful, limited changes rather than changing everything at once, while continuing appropriate medical treatment and monitoring thyroid function.
The larger question remains open: can modifying environmental or nutritional factors meaningfully change the course of Hashimoto’s disease? There are intriguing clues, but considerably more research is needed.
Key Takeaways
Hashimoto’s is an autoimmune disease, not simply a problem of low thyroid hormone.
Levothyroxine remains the standard treatment for hypothyroidism, although alternatives are sometimes considered.
Diet, selenium, vitamin D, the gut microbiome, and other factors are being studied, but the evidence varies.
A gluten-free diet is essential with celiac disease, but its benefit for Hashimoto’s without celiac disease has not been established.
Research continues into whether the underlying autoimmune process itself can be influenced.
Learn More
A clear medical overview of Hashimoto’s disease, including its causes, diagnosis, thyroid antibodies, and standard treatment.
A 2024 review of 35 studies found that selenium supplementation reduced TPO antibody levels and, in some patients, TSH, although not all measures of thyroid function improved.
Books
Kharrazian explains his functional-medicine approach to Hashimoto’s, including diet, gut health, immune regulation, and environmental factors.
A practical guide exploring nutrition, stress, gut health, infections, and environmental exposures as possible contributors to Hashimoto’s symptoms.
Videos
Explores the proposed relationship between gluten sensitivity, intestinal health, and Hashimoto’s disease.
Dr. Mark Hyman and colleagues discuss Hashimoto’s, thyroid antibodies, nutrition, gut health, environmental factors, and possible underlying contributors.