Expression of hepatocyte nuclear factor-1beta (HNF-1beta) is significantly up-regulated in ovarian clear cell carcinoma (CCC). The mechanism of up-regulation, however, remains unclear. It has been recognized that hypomethylation of specific gene promoters is involved in aberrant gene expression in carcinogenesis. In the present study, ovarian CCCs were examined whether there was a correlation between the methylation and expression status of HNF-1beta, using combined bisulfite restriction analysis (COBRA), bisulfite-sequencing and immunocyto/histochemistry. In 2 CCC cell lines, hypomethylation of HNF-1beta CpG island strongly correlated with HNF-1beta expression, at both the mRNA and protein levels. In archival surgical specimens, 20 of 20 CCCs were immunohistochemically positive for HNF-1beta, whereas none of 20 serous adenocarcinomas (SAs) or 12 normal ovaries were positive for it. By COBRA, methylation of HNF-1beta CpG island was less frequently detected in CCCs (8 of 20, 40%) than SAs (18 of 20, 90%) or normal ovaries (12 of 12, 100%) (p < 0.01), which was confirmed by bisulfite-sequencing. In addition, HNF-1beta hypomethylation correlated with a high HNF-1beta immunostaining score in CCCs. These results strongly suggest that hypomethylation of the HNF-1beta CpG island participates in the HNF-1beta up-regulation in ovarian CCC.