OBJECTIVE To study the characteristics of full-length Hepatitis B Virus (HBV) genomes isolated from patients with hepatocellular carcinoma (HCC). METHODS The full-length HBV genomes from the serum of HBsAg positive HCC patients were amplified by PCR, and then sequenced and analyzed its structure. RESULTS Twenty-two full-length HBV DNAs were obtained from different patients of HCC. Phylogenetic analysis revealed that all HBV strains could be categorized into genotype B or C and serotype adr or adw2. Structural analysis showed that HBV obtained shared meaningful consensus mutations in B/T cell epitopes of surface and core antigens, transactivating domain of X protein and enhancer II/core promoter regions as compared to standard strains. CONCLUSION Genotype and gene mutation of HBV may be closely correlated with the carcinogenesis of HBV-related hepatocellular carcinoma.