Indonesia introduced a universal vaccination program for the hepatitis B virus (HBV) in 1997; however, the longterm efficacy of the HBV vaccination has not yet been established among children. We conducted serological and genetic surveys among children in East Java, Indonesia to assess the progress of the national immunization program. A total of 185 pre-school children aged 1-5 years old born between 2006 and 2011 were enrolled in this study. A total of 150 children (81.1%) were completely vaccinated, and the birth dose coverage within 7 days after birth was 74%. None of the children were positive for the hepatitis B surface antigen (HBsAg), while 4 children were infected with occult HBV. The prevalence of anti-HBs antibody positive was only 26.5%, and positive prevalence and titer of anti-HBs decreased with age. The universal HB vaccination is considered effective in preventing HBV infection in children in this study site, while the protective rate remains insufficient. An effective strategy needs to be developed in order to detect all vaccination failure cases. To achieve complete protection, it would be necessary to consider an appropriate time for the first dose and booster dose.