In Taiwan, decrease of both infection and carrier rates of hepatitis B virus (HBV) have been documented especially in metropolitan areas after universal HBV vaccination. This study investigated HBV infection status in a rural township 15 years after the program began. Three cross-sectional studies were conducted in 1999, 2000 and 2003, to recruit all the students of the only junior middle school, born from July 1984 to June 1991, in a township in central Taiwan. Serum samples were tested for HBsAg, anti-HBs and anti-HBc. Subjects identified to be neither positive for HBsAg nor anti-HBs were given a booster dose of HBV vaccine. Subjects lacking an anamnestic anti-HBs response were given a complete 3-dose vaccination. A total of 1454 (98.5%) students responded. The prevalence rate of HBsAg decreased 57% [from 12.5% in 1984 to 5.4% in 1991, P < 0.005 (chi2-test for linear trends)], and anti-HBc positive rate dropped 68% (from 31.9 to 10.2%, P < 0.001). An anamnestic anti-HBs response developed after a vaccine booster among 433 (72%) anti-HBs negative and 12 (66.7%) anti-HBc alone subjects. And 93 (94.9%) anti-HBs negative and 1 (16.7%) anti-HBc alone subject developed a primary anti-HBs response after catch-up vaccination. Viremia was detected for two anti-HBc alone subjects without anamnestic or primary response. The vaccination program has decreased the number of those infected and carrier rates in either urban or rural areas in Taiwan. However, the prevalence of HBsAg and anti-HBc in rural area were much higher than urban area.