Recent studies suggest that epigenetic mechanisms are not only essential for the dynamic transcriptional regulation in embryonic and somatic stem cells, but are also actively involved in tumorigenesis: genes important for pluripotency are epigenetically regulated and aberrant epigenetic changes have been detected in virtually all human malignancies studied, including Hepatocellular Carcinoma (HCC). Infection with Hepatitis C Virus (HCV) is a major risk factor for the development of HCC. Despite the fact that HCV is a RNA virus without a DNA intermediate, recent studies demonstrate that HCV viral proteins may actively participate in epigenetic regulation of hepatic cancer stem cell phenotypes and induce HCC-specific epigenetic changes. Identification of host epigenetic alterations induced by HCV infection and epigenetic differences between hepatic cancer stem cells and the bulk non-tumorigenic cancer cells, may yield potential biomarkers for early detection, as well as therapeutic targets for HCV associated HCC.