Karyotyping of human liver cancer cell lines and chromosome in situ hybridization of hepatitis B virus (HBV) DNA was performed in order to elucidate the possible mechanism of hepatocarcinogenesis from evidence of chromosomal changes and HBV integration patterns. HepG2-2 and HepG2-5 cell lines were HepG2 cells experimentally transfected with HBV DNA; the HCC36 cell line was derived from a hepatocellular carcinoma containing integrated HBV DNA from a Taiwanese patient. HepG2 cells, a hepatoblastoma cell line without HBV DNA integration, served as negative control. In HepG2-2, HepG2-5, and HCC36 cells, multiple integrations of HBV DNA were observed by in situ hybridization and hybridization signals occurred preferentially on certain chromosomes: 2, 5, 10, 11, 18; 7, 10, 13, 17, 18; and 4, 6, 11, 12q+, 18; respectively. In addition, a strong correlation between chromosomal changes and HBV integration was noticed in HCC36 cells, especially at chromosome 12q+.