Autoimmune disease. The most common cause of hypothyroidism is an autoimmune disorder known as Hashimoto's thyroiditis. Autoimmune disorders occur when your immune system produces antibodies that attack your own tissues. Sometimes this process involves your thyroid gland.
Scientists aren't sure why this happens, but it's likely a combination of factors, such as your genes and an environmental trigger. However it happens, these antibodies affect the thyroid's ability to produce hormones.