Epigenetic alternation via the promoter hypermethylation of putative tumor suppressor genes has been implicated in the development of hepatocellular carcinoma (HCC). In this study, we investigated the epigenetic changes in two candidate tumor suppressor genes, endothelin receptor type B (EDNRB) and p16, and their relation to the expression of these two genes in HCC. Methylation-specific polymerase chain reaction (MS-PCR) was performed to analyze the promoter methylation status of the EDNRB and p16 genes in tumors and paired non-tumor liver portions of 34 HCC patients. The mRNA expression was assessed by reverse transcription-PCR assay. Hypermethylation of the EDNRB and p16 genes was detected in 29.4% (10/34) and 32.3% (11/34) of HCC patients, respectively. Moreover, the reduction of mRNA expression was correlated to the promoter hypermethylation of the EDNRB and p16 genes. In conclusion, aberrant methylation of EDNRB and p16 genes is highly prevalent in HCC. It suggested that epigenetic alteration of the EDNRB and p16 genes may play an important role in the pathogenesis of HCC.