To identify methylation-mediated silencing of genes in hepatocellular carcinoma (HCC), we surveyed genes induced by treatment with 5-aza-2'-deoxycytidine (5-Aza-CdR) in six human hepatoma cell lines using cDNA microarray analysis and determined the methylation status of 5' CpG islands by bisulfite DNA sequencing or methylation-specific PCR. Fifty genes exhibited a >5-fold induction in response to treatment with 5-Aza-CdR in at least one of the hepatoma cell lines examined. Among these genes, the hepatocyte growth factor activator inhibitor 2/placental bikunin (HAI-2/PB) gene was maximally induced by 5-Aza-CdR in three of six cell lines studied (HLE, HuH7, and Hep3B). Bisulfite sequencing revealed that the 5' CpG island of this gene was densely methylated in HLE, HuH7, and Hep3B cells. After treatment with 5-Aza-CdR, re-expression and demethylation of HAI-2/PB gene were detected in these cells. These findings suggest that HAI-2/PB expression may be inappropriately repressed by promoter hypermethylation in HCC. Methylation-specific PCR analysis demonstrated that HAI-2/PB hypermethylation occurred in 21 of 26 HCC tumors (80.8%), whereas in the corresponding nontumorous liver tissues, it was found in 7 of 26 samples (26.9%). In addition, HAI-2/PB hypermethylation was not detected in any of the seven normal liver samples from individuals without HCC. Reverse transcription-PCR analysis demonstrated that promoter hypermethylation was associated with the reduced expression of the HAI-2/PB gene in HCC tumors. In conclusion, we have found that the HAI-2/PB gene is silenced by promoter hypermethylation in human hepatoma cells by means of cDNA microarray analysis after 5-Aza-CdR treatment, and that HAI-2/PB hypermethylation occurs frequently in primary HCC tumors.