The autoimmune thyroid diseases with the main phenotypes Graves' disease and Hashimoto's thyroiditis belong to the most frequently occurring autoimmune diseases. Genetic factors play a major role in their etiology, and in the past a couple of susceptibility genes have been identified. These are immunoregulatory genes like the HLA class II genes, the CTLA-4 gene and the PTPN22 gene and thyroid-specific genes for the TSH receptor and thyroglobulin. Even though this knowledge contributed to a better understanding of the pathogenesis of the autoimmune thyroid diseases, up to now the clinical relevance has been discussed insufficiently. Hence, this review provides an update of all relevant susceptibility genes for thyroid autoimmunity and discusses their significance for the clinical work.