The etiology of the autoimmune thyroid diseases (AITDs), Graves' disease (GD) and Hashimoto's thyroiditis (HT) is largely unknown. However, genetic susceptibility is believed to play a major role. Recently, Chu et al. conducted a genome-wide association study in a Chinese Han population and identified two novel GD susceptibility loci within 4p14 (rs6832151) and 6q27 (rs9355610). The objective of the study was to replicate these associations in a Japanese population. We analyzed rs6832151 and rs9355610 genotypes in a case-control study based on 457 Japanese AITD patients (286 GD and 171 HT patients) and 222 matched Japanese controls using the high-resolution melting and unlabeled probe methods. Case-control association studies were performed using the c² and Fisher's exact tests with Yates correction. We found a significant allelic association between AITD and rs9355610 located in 6q27 (p = 0.023). GD was significantly associated with this SNP (p = 0.0055), while HT showed no significant associations with any SNPs. Moreover, when patients with GD were stratified according to Graves' ophthalmopathy (GO), there were no allelic associations with GO. These findings suggest the presence of AITD susceptibilty genes, especially in distinct subgroups of GD, in or near 6q27.