Objective To compare the performance of Inverse-PCR, Alu-PCR and Cassetteligation-mediated PCR (CLM-PCR) in HBV DNA integration sites identification. Mehtods One HCC biopsy was obtained from surgically resected sample. The patient was positive for serum hepatitis B surface antigen (HBsAg). The genomic DNA was purified by the standard phenol/chloroform extraction and ethanol precipitation method. Seperated set of primers were designed to amplify the HBV DNA integration region by means of 3 different PCR methods respectively. The PCR products were analyzed by electrophoresis, then cloned to PMD18-T vector for DNA sequencing. The sequence alignment was performed under Blast software. Results 7 bands and 22 sequencing results was obtained from IPCR and 3 integration sites was identified. Alu-PCR provided 12 bands and 32 sequencing results, and CLM-PCR showed 12 bands and 4sequencing results. No integration site was identified from the latter two. Conclution IPCR compared with another two methods showed a reliable capacity in HBV DNA integration site identification.