Thyroid autoantigens have been well studied in view of the identification corresponding to respective autoantibodies in circulation, which are utilized as a diagnostic or follow-up marker of autoimmune thyroid diseases. There are several thyroid autoantigen genes cloned, such as thyroglobulin (TG), thyroid peroxidase (TPO), thyrotropin receptor (TSHR) and iodine transporter (NIS). Recent progress of the molecular study on thyroid autoantigens has allowed us to examine the characteristic features of these genes. Here we introduce the four representative thyroid autoantigens (TG, TPO, TSHR and NIS) and summarize the specific findings of genetic alteration and the sites of antigenicity corresponding to autoantibodies.