Epigenetic inactivation by aberrant DNA methylation has been reported for many microRNA genes in various human malignancies. However, relatively little is known about microRNA gene methylation in hepatocellular carcinoma (HCC). Therefore, a systematic screen for identification of aberrantly hypermethylated microRNA genes in HCC was initiated. The methylation status of 39 intergenic CpG island associated microRNA genes was analyzed in HCC cell lines (n = 7), immortalized hepatocytes (n = 2) and normal liver samples (n = 5). Subsequently, 13 differentially methylated microRNA genes were analyzed in primary human HCC samples (n = 40), benign liver tumors (n = 15) and the adjacent liver tissues employing pyrosequencing. Expression of microRNA genes was measured using quantitative real‐time polymerase chain reaction (RT‐PCR). In addition, DNA methylation and expression of microRNA genes were measured after DNMT1 knockdown or DNMT inhibition. Aberrant hypermethylation and concomitant reduction in expression of intergenic microRNA genes is a frequent event in human HCC: hsa‐mir‐9‐2 (23%), hsa‐mir‐9‐3 (50 %), hsa‐mir‐124‐1 (20%), hsa‐mir‐124‐2 (13%), hsa‐mir‐124‐3 (43%), hsa‐mir‐129‐2 (58%), hsa‐mir‐596 (28%) and hsa‐mir‐1247 (38%). Altogether, it affects 90% of the HCC specimens under study. MicroRNA gene methylation is not found in hepatocellular adenoma (n = 10) and focal nodular hyperplasia (n = 5). DNMT1 knockdown or DNMT inhibition reduced microRNA gene methylation and stimulated expression. In primary human HCC specimens hypermethylation and expression of microRNA genes showed an inverse correlation. Concordant hypermethylation of three or more microRNA genes is a highly specific marker for the detection of HCC and for poor prognosis. What's new? Inactivation of miRNAs by methylation occurs in various cancers, but little is known so far about methylation of miRNAs in liver cancer. In this study, the authors compared the methylation status of 13 differentially methylated miRNAs in primary hepatocellular carcinoma, benign liver tumors, and normal liver specimens. They found epigenetic inactivation by methylation in most of the cancer cell lines. This hypermethylation could be used to distinguish between cancerous and benign liver tumors.