Autoimmune disorders of the thyroid such as Graves' disease and Hashimoto's thyroiditis are the most common autoimmune diseases in the Western world. The frequent occurrence of both diseases in members of the same family indicates the influence of common genetic factors generally predisposing to thyroid autoimmunity. Common susceptibility loci have been mapped to the HLA region on chromosome 6p21 (HLA DR, HLA DQ), to chromosome 2q33 (CTLA4) and possibly to chromosome 8q24 (thyroglobulin). Additional susceptibility is conferred by genomic variants of the vitamin D system (vitamin D receptor and CYP1 alpha hydroxylase). Since these polymorphisms prevail also in healthy relatives they are necessary but not sufficient cofactors. The higher prevalence of thyroid autoimmune disease in women cannot be explained by susceptibility genes. The observation of microchimerisms in thyroid tissue might explain that an immunisation by fetal-maternal interaction can lead to thyroid autoimmunity in HLA risk combinations.