Hepatocellular carcinoma (HCC) is one of the most aggressive malignancies in humans, and its prognosis is generally poor even after surgery. The zinc finger of the cerebellum (ZIC1) gene is a novel tumor suppressor gene that plays a crucial role in vertebrate development. Altered expression of ZIC1 is observed in various types of human cancers. The aims of the present study were to investigate the methylation status of ZIC1 in HCC and evaluate its clinical implication. The methylation status of ZIC1 was analyzed in 132 pairs of HCC and corresponding noncancerous tissues by methylation-specific polymerase chain reaction (PCR) (MSP). The expression of ZIC1 messenger RNA (mRNA) in HCC tissues was examined by real-time PCR. Methylation frequency of ZIC1 in HCC was significantly higher than that in the corresponding noncancerous tissues (P < 0.001), and it was correlated with tumor size (P = 0.022), histological differentiation (P = 0.033), and tumor stage (P = 0.009). The downregulation of the ZIC1 mRNA expression in HCC was correlated with the ZIC1 methylation (P < 0.001). The patients with methylated ZIC1 had a poorer overall survival than those without methylated ZIC1 (P < 0.001). Taken together, our results suggested that the hypermethylation may lead to promoter silencing of ZIC1 mRNA and associated with poor survival in HCC. Overall, aberrant methylation is an important mechanism for ZIC1 inactivation in HCC, and ZIC1 methylation may be a promising biomarker for the diagnosis and prognosis of HCC.