As part of a genome scan to locate familial Graves' disease (GD) and Hashimoto's thyroiditis (HT) genes, an autoimmune thyroid disease (AITD) susceptibility locus has recently been identified at 5q31-q33 in a Japanese population. We performed an association study using six microsatellite markers located at this locus in a set of 440 unrelated Japanese AITD patients and 218 Japanese controls. We found significant allelic association between AITD and three markers located in 5q23-q33. GD demonstrated significant associations with two of these markers, while HT did not show significant associations with any markers. Further, when patients with GD were stratified according to clinical manifestations, the association was significantly different from the other subgroup of each category. These findings suggest the presence of susceptible genes of AITD, especially distinct subgroups of GD, in or near 5q23-q33.