The implementation of the Expanded Program of Immunization (EPI) in 1989 has dramatic impact on hepatitis B virus (HBV) infection in school children in Malaysia. A cross-sectional seroprevalence study of HBV infection in 190,077 school children aged 7-12 years from 1997 to 2003 showed a steady decline of HBV surface antigen (HBsAg) prevalence rate from 2.5% for children born in 1985 to 0.4% among school children born in 1996. The overall prevalence of HBsAg was 0.6%, 0.7% in males and 0.6% in females. Over 92.7% of school children had been vaccinated with HBV vaccine, in which 93.7% were vaccinated under the EPI and 6.3% on voluntary basis. The school children vaccinated under EPI had a 0.4% HBsAg carrier rate, which was significantly lower than school children vaccinated on a voluntary basis (HBsAg carrier rate 1.3%) and non-vaccinated school children (HBsAg carrier rate 2.7%), suggesting that HBV vaccination of infants was the most effective measure in preventing vertical transmission of HBV in the hyperendemic region.