The government of Japan started a selective vaccination programme to prevent mother-to-infant infection by hepatitis B virus (HBV) since January 1986. The effect of the programme on first-time blood donors has not been examined in detail. Data of first-time blood donors aged 16–25 years from 1996 to 2007 were extracted from the Japanese Red Cross (JRC) donors' database. Principal component analysis (PCA) was used to visualize the birth-year-dependent group of rate of HBV-positive donors. According to the birth of year, donors were divided into four groups by PCA. After the start of the programme, donors born in 1986–1989 comprised a single group. Before the start of the programme, three groups (1980, 1981–1984 and 1985) were identified. Although a significant time-dependent decrease in the rate of HBV-positive donors was observed before the start of the programme, a significant difference in the rate of HBV-positive donors was observed around the start of the programme by regression analysis for 16–19-year-old first-time blood donors. The selective vaccination programme has been effective to prevent the vertical transmission of HBV from the analysis of first-time blood donors. On the other hand, vaccination of blood donors should be considered to reduce the risk of post-transfusion HBV infection, because the horizontal transmission increases in HBV-positive blood donors.