It is still unclear as to whether the gene expression pro®le in HCV-or HBV-related HCC exhibits a degree of speci®city and whether the development of HCC in a context of cirrhosis in¯uences this gene pro®le. To address these issues, the expression pro®les of 15 cases of HCC were analysed using cDNA macroarray. A global analysis and hierarchical clustering, demonstrated the heterogeneity of HCC patterns, with a majority of down-regulated genes. Statistical analysis clearly showed a distinction between the gene expression pro®les of HCV-and HBV-related HCC. HBV-associated HCC exhibited involvement of dierent cellular pathways, those controlling apoptosis, p53 signalling and G1/S transition. In HCV-related HCC we identi®ed a more heterogenous pattern with an over-expression of the TGF-beta induced gene. In HCC developing on noncirrhotic tissues, beta-catenin encoding gene and genes implicated in the PKC pathway were speci®cally upregulated. In addition, our investigation highlighted a distinct pro®les of TGF-beta superfamily encoding genes in well, moderately or poorly dierentiated HCC. Overall, our study supports the hypothesis that despite the heterogeneity of the HCC pattern, the large-scale screening of gene expression may provide data signi®cant to our understanding of the mechanism of liver carcinogenesis.