Hepatocellular carcinoma (HCC) is among the fifth most common cancers worldwide. Its incidence is still rising in part because of the high level of hepatitis C virus infection. Tumor markers currently used such as serum alpha-foetoprotein are not sufficient for diagnosis of the tumor and satisfying follow-up of the patients. Mechanisms of hepatocarcinogenesis ar not completely understood although several altered genes have been described in HCC. The genetic changes involved can be divided in at least 4 different pathways, each pathway contributing to a limited number of tumors. These are: 1) the p53 pathway involved in response to DNA damage, 2) the retinoblastoma pathway involved in the control of the cell cycle, 3) the transforming growth factor-beta (TGF-beta) pathway involved in growth inhibition, and 4) the Wnt pathway involved in cell-cell adhesion and signal transduction. Alterations of the epigenetic regulation of gene expression have also been described. Evolution of molecular biology methods tends to the development of more global genomic approaches; microsatellite instability analysis, chromosomal instability analysis or gene expression profile analysis have been used to investigate HCC. Finally, attempts to develop molecular biomarkers based on peripheral blood analysis more easily accessible in clinical routine patients have also been developed.