Hashimoto thyroiditis affects 1 to 2 percent of people in the United States. It occurs more often in women than in men, which may be related to hormonal factors. The condition is the most common cause of thyroid underactivity (hypothyroidism) in the United States.

Hashimoto thyroiditis is thought to result from a combination of genetic and environmental factors. Some of these factors have been identified, but many remain unknown.

Hashimoto thyroiditis is classified as an autoimmune disorder, one of a large group of conditions that occur when the immune system attacks the body's own tissues and organs. In people with Hashimoto thyroiditis, white blood cells called lymphocytes accumulate abnormally in the thyroid, which can damage it. The lymphocytes make immune system proteins called antibodies that attack and destroy thyroid cells. When too many thyroid cells become damaged or die, the thyroid can no longer make enough hormones to regulate body functions. This shortage of thyroid hormones underlies the signs and symptoms of Hashimoto thyroiditis. However, some people with thyroid antibodies never develop hypothyroidism or experience any related signs or symptoms.

People with Hashimoto thyroiditis have an increased risk of developing other autoimmune disorders, including vitiligo, rheumatoid arthritis, Addison disease, type 1 diabetes, multiple sclerosis, and pernicious anemia.

Variations in several genes have been studied as possible risk factors for Hashimoto thyroiditis. Some of these genes are part of a family called the human leukocyte antigen (HLA) complex. The HLA complex helps the immune system distinguish the body's own proteins from proteins made by foreign invaders (such as viruses and bacteria). Other genes that have been associated with Hashimoto thyroiditis help regulate the immune system or are involved in normal thyroid function. Most of the genetic variations that have been discovered are thought to have a small impact on a person's overall risk of developing this condition.

Other, nongenetic factors also play a role in Hashimoto thyroiditis. These factors may trigger the condition in people who are at risk, although the mechanism is unclear. Potential triggers include changes in sex hormones (particularly in women), viral infections, certain medications, exposure to ionizing radiation, eating large amounts of foods that contain animal proteins, and excess consumption of iodine (a substance involved in thyroid hormone production).