Selenium (Se) takes part in the activation and deactivation of thyroid hormones as a component of the catalytic site of selenodeiodinases and plays an important role in thyroid protection against oxidative damage. Based on these assumptions, in the last 10 years, several clinical trials have evaluated the effects of Se supplementation in patients with autoimmune thyroid disease (AIT) with not conclusive results. This review aims to analyze the effects of Se supplementation in patients with AIT considering studies published on this subject, so far. The emphasis is especially given on the multifactorial genesis of Hashimoto's thyroiditis (HT), which can affect the action of selenoproteins, and on the poor correlation between thyroid structural damage in HT, measurable by ultrasound examination, and antibody titer, suggesting possible recommendations for future studies.