AIM: Growing evidence demonstrates that hepatitis B virus (HBV) integration and re-sultant de novo genetic mutations play an important role on tumorigenesis and malig-nant progression of hepatocellular carcinomas (HCCs). In the present study, we sought to address the impact of HBV integration on the genome of the host cell. METHODS: We employed genome-wide oligo-array comparative genomic hybridiza-tion (CGH) to profile genetic copy number alterations (CNAs), including deletion or am-plification, within genomes of parental HepG2 cells and the HBV-transfected variant, HepG2215. To determine whether or not the selection pressure during establishing stable transfectant contributed to genetic alteration, another HepG2 variant, HepG2.2 cells, previously transfected with a HBV-unrelated gene followed by G418 selection was also included in our experiments. Results were validated by dye-swap experiments. RESULTS: Extensive de novo genetic aberrations have been detected In HepG2215 cells but not present in HepG2 cells and HepG2.2 cells, such as gains on chromosome arms 8q, 9q, 11p, 12q, 14q, 15q, 19p, 21q, 22q and losses on 8p, 8q, 9p, 9q, 11p, 11q, 12p, 12q, 14q, 15q, 18p, 18q, 19p, 19q, 21q, 22q. It is noteworthy that chromosome 8 harbored several de novo CNAs in comparison with those of HepG2. In addition, genes implicated in cell cycle control, apoptosis, tumorigenesis and malignant progression have been assigned to these altered regions. CONCLUSION: Our results demonstrate that HepG2215 cells harbored de novo CNAs at several sites in comparison with parental HepG2 cells. There was no significant dif-ference between the genetic profile of HepG2 and HepG2.2 cells, indicating the new ge-netic aberrations were not generated by G418 selection. The genome instability of HepG2215 cells could be a result of HBV DNA integration or arised from the trans-acting of viral gene product. These findings provide important information on application of HepG2215 cells and support the hypothesis that HBV infection associates with devel-opment of some HCCs by interfering with cellular processes responsible for the insta-bility of genome. Journal of Cancer Molecules 1(2): 93-98, 2005.