The genetic basis of autoimmune thyroid disease (AITD), which includes Graves’ disease (GD) and Hashimoto’s thyroiditis (HT), is thought to be polygenic. The genetic factors have been shown by twin studies and familial aggregation, including clustering of GD and HT within the same families. While the genetic basis of AITD is unclear, it is believed to be polygenic. Identification of genetic factors will contribute to not only the understanding of pathogenesis of AITD, but also the prevention and treatment of the diseases. Several genetic factors associated with AITD susceptibility have been tentatively identified. Some are molecules related to immune responses including the human leukocyte antigen (HLA) and the cytotoxic T lymphocyte associated-4 (CTLA-4) genes. Others are those related to thyroid-specific autoantigens including the thyrotropin receptor (TSHR) gene. As part of a genome scan to locate familial GD and HT genes, other additional chromosomal locations including chromosome 8q and 5q have been reported in a Japanese population. As the next step, ZFAT (zinc-finger gene in AITD susceptibility region) gene was identified as one of the susceptibility genes in 8q23-q24. In addition, we found that a particular allele of intron 7 or near this region of the TSHR gene may contribute to GD susceptibility. Here, I introduce our recent studies on genetics of AITD.