The balance between apoptosis and cell proliferation is the key determinant in the pathogenesis of many diseases including autoimmune thyroiditis. In recent years, many studies have strengthened the concept that pro- and anti-apoptotic molecules expressed in thyroid epithelial cells as well as in thyroid infiltrating lymphocytes play a pivotal role in the pathogenesis and/or progression of autoimmune thyroiditis. In this review, the role of apoptosis in the pathogenesis in the two well-defined murine models of autoimmune thyroiditis, experimental autoimmune thyroiditis (EAT) and iodine-induced autoimmune thyroiditis (IAT) is discussed. Recent important patents focusing on apoptosis as novel therapeutic targets are also discussed in this review. Further clinical trials are needed to evaluate the efficacy and safety of these agents.