Since the national program of immunoprophylaxis against perinatal transmission of hepatitis B virus (HBV) was started in 1986, the HBV carrier rate in children was dramatically decreased. However, the cases of failure of the prevention still exist. In this study, we retrospectively analyzed the reasons of 56 cases of the failure of the prevention after the initiation of national program. Seventeen (31%) were not received the immunoprophylaxis of the national program by mistake. Seven (12%) were received the inappropriate doses of schedule. Our national program is relatively complicated compared to the method adopted by almost all other countries. Because of the universal vaccination program is easy to finish the schedule, we should consider converting our prevention schedule to the universal vaccination program.