This study aimed to investigate the primary immunogenicity and the long-term efficacy of recombinant hepatitis B virus (HBV) vaccine in biliary atresia (BA) children. Fifty BA infants (age, 11 +/- 3.9 mo), and 23 BA patients at childhood (age, 8.5 +/- 0.22 y) were included for the evaluation of HBV surface antibody (anti-HBs) levels after three doses of recombinant HBV vaccine immunization. Age- and gender-matched healthy infants (n = 50) and children (n = 23) were enrolled as the control group. Serum samples of the study populations were collected for HBV seromarkers determination. In the absence of hepatitis B virus core antibody and HBV surface antigen, serum anti-HBs level above 10 IU/L was considered adequate immunogenicity to HBV vaccine. The prevalence of adequate anti-HBs levels after recombinant HBV vaccine in BA infants was significantly lower than those of the controls (p = 0.006). There was no difference in the prevalence between childhood BA patients and their matched controls (p = 0.538). In conclusion, adequate primary humoral immunity after the standard doses of recombinant HBV vaccine in BA infants is hard to establish. However, once immunity is acquired, BA children have adequate anti-HBs titer in the long run.