Objective To investigate the association of hepatitis B virus(HBV) S gene quasispecies with the outcome of HBV infection.Methods Serum samples were collected from three chronic HBV carriers, three chronic hepatitis B and three chronic severe hepatitis B patients.All subjects were male and with HBV genotype C.HBV S gene was amplified, and 20 clones of HBV fragment were randomly selected and sequenced from each sample.SPSS 15.0 software was adopted for analysis.Results Quasispecies complexity of HBV S gene in chronic HBV carriers and chronic hepatitis B tended lower than that of the severe chronic hepatitis B, but the difference was not of statistical significance (P＞0.05).In T cell epitope 45, 47, 85 amino acid sites of the HBV S gene, the constitution of quasispecies in the chronic hepatitis B was more complex than that of the HBV carriers (P=0.01), but compared with the severe chronic hepatitis, the difference was not significant (P=0.06).The computer model showed that both the dominant clones and the non dominant clones could effectively bind to the receptors of cytotoxic T lymphocytes.Conclusion Quasispecies in some T cell epitopes of HBV S gene may be related with the clinical outcome of hepatitis B.