OBJECTIVE To evaluate the efficacy of hepatitis B viruse (HBV) vaccination and its influencing factors among children in rural area of Jiangsu province. METHODS Twenty-five hundred and twenty-two children born after 1998 in rural area were selected as the study population using multistage cluster sampling method. HBsAg and anti-HBs were detected by enzyme linked immunoassay (ELISA) and radio-immunoassay (RIA), respectively. Anti-HBs negative children were boosted using different hepatitis B vaccines and the efficacy was compared. Factors causing HBV infection in HBsAg positive children were also investigated. RESULTS HBsAg positive rates in 1-7 year olds were 0.28%-1.28%, and the anti-HBs positive rates decreased from 76.7% to 45.5%. The HBsAg positive rate in children not timely vaccinated was significantly higher than those with HBV vaccine injection within 24 hours after birth (1.4% vs. 0.5%, P = 0.031). More than 90% of the anti-HBs negative children had protective level of anti-HBs after boosted with HBV vaccine. CONCLUSIONS HBsAg positive rate in children born after 1998 in rural area of Jiangsu province decreased significantly, with an average of 0.8%. The reason for HBsAg carriage in children might be attributed to mother-to-infant transmission or not timely HBV vaccination.