Hepatitis B virus (HBV) DNA is often integrated intohepatocellular carcinoma (HCC). Although the relationshipbetween HBV integration and HCC development has beenwidely studied, the role of HBV integration in HCCdevelopment is still not completely understood. In the presentstudy, we constructed a pooled BAC library of 9 establishedcell lines derived from HCC patients with HBV infections. Byamplifying viral genes and superpooling of BAC clones, weidentified 2 clones harboring integrated HBV DNA. Screeningof host-virus junctions by repeated sequencing revealed anHBV DNA integration site on chromosome 11q13 in theSNU-886 cell line. The structure and rearrangement ofintegrated HBV DNA were extensively analyzed. An invertedduplicated structure, with fusion of at least 2 HBV DNAmolecules in opposite orientations, was identified in theregion. The gene expression of cancer-related genes increasednear the viral integration site in HCC cell line SNU-886.