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Background The public vaccination program of hepatitis B virus (HBV) was launched during 1984 in Taiwan, China.However, the long-lasting protective efficacy of HBV vaccination among adolescents older than 15 years of age was seldom recorded.Methods A seroepidemiological survey was conducted among 4575 first-year university students in Taiwan, China during 2000 to 2003, including the serological data of HBV by testing HBV surface antigen (HBsAg), surface antibody (anti-HBs), HBV core antibody (anti-HBc) and demographic information.Results HBsAg carrier rate among male university students born before the initiation of the HBV vaccination program decreased from 12.8% to 4.8% among those born after the vaccination program (P＜0.001, X2 test for linear trend).Similarly, HBsAg carrier rate among female university students born before the initiation of the HBV vaccination program decreased from 8.1% to 2.7% among those born after the vaccination program (P＜0.001, X2 test for linear trend). Both male and female students in eastern Taiwan had the highest HBsAg carrier rate compared with the other places. Using multiple logistic regression analysis, compared with students born after July 1984, the adjusted OR of HBsAg carrier rate decreased from 3.10 for students born before June 1981 to 1.56 for students born from July 1983 to June 1984 (95%CI 1.96-4.91, P＜0.001; 95%C/1.06-2.28, P=0.024; respectively).Conclusions Public vaccination provides long-lasting protection again HBV infection among the university students in Taiwan, China older than 18 years of age. There is a geographic variation of HBV infection among young adults in Taiwan,China.