Objective To analyze the sequence of Pre-S gene in asymptomatic chronic HBV carriers (ASCs) with low-level HBsAg.Methods The serum samples were collected from 654 ASCs in the First Affiliated Hospital of Zhejiang University School of Medicine , Hangzhou Sixth People’s Hospital and the 903th Hospital of PLA.According to the level of HBsAg , ASCs were divided into low-level HBsAg group (≤10 IU／mL ) and high-level HBsAg group (＞10 IU／mL ).The pre-S／S gene amplification and sequencing were performed in 138 ASCs with low-level HBsAg and 100 age-matched ASCs with high-level HBsAg.A phylogenetic tree was constructed to determine the genotype , based on the successful sequencing results of Pre-S gene in the high level HBsAg group , the Pre-S gene reference sequences of the main ASCs genotypes in Eastern China were established.The sequence of Pre-S gene in low-level HBsAg group was analyzed and compared with the reference sequences.SPSS 12.01 statistical software was used to analyze the data.Results Sixty-three cases of Pre-S／S were successfully sequenced in 138 ASCs of low-level HBsAg group, including 52 cases of B genotype and 11 cases of C genotype.Among the 100 cases of high-level HBsAg group, 94 cases of Pre-S／S were successfully sequenced , including 48 cases of B genotype and 46 cases of C genotype.The sequence analysis indicated that in the B genotype , 81 amino acid mutation sites were found in the Pre-S protein of the low-level HBsAg group, including 4 significant mutations: F56I／V, T76A／N／P in the Pre-S1 region, P15L／S／T and Y21T／F／H／N in the Pre-S2 region; while 47 amino acid mutation sites were found in Pre-S protein of high-level HBsAg group, including 3 significant mutations :L34F, V49A and P59S／L in Pre-S1 region.The total number of amino acid mutation sites in the low-level HBsAg group of B genotype was higher than that of the high-level HBsAg group (χ2 ＝14.008, P＜0.05). In the C genotype, 19 amino acid mutation sites were found in the Pre-S protein of the low-level HBsAg group, including 3 significant mutations : W66V／G and A79V in the Pre-S1 region,V32A in the Pre-S2 region; while 39 amino acid mutation sites were found in Pre-S protein of the high-level HBsAg group, including 2 significant mutations: A79V in Pre-S1 region and T49I in Pre-S2 region.The total number of amino acid mutation sites of Pre-S protein in the C genotype was significantly different between the two groups (χ2 ＝7.571, P＜0.05).Conclusion Significant mutations in Pre-S gene may be associated with the persistent expression of low-level HBsAg in ASCs.