Objective To determine the hepatitis B immunoprophylactic failure rate in infants born to hepatitis B virus(HBV) infected mothers and to characterize HBV genes. Methods HBV-serological testing was conducted for pregnant women and infants. The complete genomes of 30 HBV isolates were sequenced, and genetic characteristics were analyzed using MEGA 5 software. Results The immunoprophylactic failure rate for infants who had completed the scheduled hepatitis B vaccination program was 5.76%(32/556). High sequence homology(99.8%-100%) was observed in 8 of the 10 mother-infant pairs. We identified 19 subgenotype C2 strains, 9 subgenotype B2 strains, and 2 subgenotype C1 strains. Three serotypes were detected: adr(19/30), adw(9/30), and ayw(2/30). The frequency of amino acid mutation of the ‘a’ determinant region was 16.67%(5/30), including that of Q129 H, F134 Y, S136 Y, and G145 E. We detected 67 amino acid mutations in the basal core promoter, precore, and core regions of the genome. Conclusion The immunoprophylactic failure rate in infants born to HBV-infected mothers is low in the regions of China examined during this study. Moreover, HBV mutation in the ‘a’ determinant region could not account for immunoprophylactic failure for all infants. Objective To determine the hepatitis B immunoprophylactic failure rate in infants born to hepatitis B virus (HBV) infected mothers and to characterize HBV genes. Methods HBV-serological testing was conducted for pregnant women and infants. The complete genomes of 30 HBV isolates were sequenced, and the genetic characteristics were analyzed using MEGA 5 software. Results The immunoprophylactic failure rate for infants who had completed the scheduled hepatitis B vaccination program was 5.76% (32/556). High sequence homology (99.8% -100%) was observed in 8 of We identified 19 subgenotype C2, 9 subgenotype B2, and 2 subgenotype C1. Three serotypes were detected: adr (19/30), adw (9/30), and ayw (2/30 The frequency of amino acid mutation of the ’a’ determinant region was 16.67% (5/30), including that of Q129 H, F134 Y, S136 Y, and G145 E. We detected 67 amino acid mutations in the basal core promoter, precore, and core regions of the genome. Concl usion The immunoprophylactic failure rate in infants born to HBV-infected mothers is low in the regions of China examined in this study. Moreover, HBV mutation in the ’a’ determinant region could not account for immunoprophylactic failure for all infants.