Abstract： Objective To investigate the molecular epidemiology of hepatitis B virus(HBV) in child carriers. Methods Blood samples were collected from children under 15 in Jiangsu and Zhejiang provinces. Enzyme immunoassay(EIA) and microparticle enzyme immunoassay(MEIA) were applied to screen hepatitis B surface antigen(HBsAg) positive children. Nested-PCR and real time PCR were used to amplify the HBV S gene and detected HBV DNA loads. S gene sequence and three-dimensional structure were analyzed by the DNASTAR and VMD1.8.6, respectively. SPSS 12.0 software was applied for data processing. Results A total of 64 HBsAg-positive cases were found in the screened children, from which 41 HBV S gene sequences were obtained. The average HBV DNA loads were(4.15±0.79)×10~7 copies/mL in 64 HBV carriers. Among 41 sequences. genotype C, B and B+C accounted for 82.93%(34/41), 12.19%(5/41)and 4.88%(2/41), respectively; and the serotypes were adr(34/39,87.18%), adw(4/39,10.24%) and ayr (1/39, 2.56%) with 2 strains unable to be sub-typed. The most common variants of "a" determinant in HBV S gene were 129 site Q→F(glutamine→phenylalanine), 145 site G→R(glycine→lysine), 131 site S→N(serine→asparagine)and 144 site C→A(cysteine→alanine), and the mutation frequencies were 12.20%(5/41), 4.88%(2/41), 2.27%(1/41)and 2.27%(1/41), respectively . The total mutation frequency was 21.95%(9/41). The S protein spatial structures of 129 site "Q→F" and 145 site "G→R" were entirely different from that of the wild strain. Conclusion Wild strain of HBV(C/adr) is predominant in the children HBV carriers, exhibiting a high replication, and the HBV vaccine should be still effective.