Liver cancer is one of the three most common causes of cancer mortality in the world and it is closely related to chronic hepatitis B viral(HBV) infection in Korea. The decline of HBV prevalence for the last two decades in Korea might be partly due to the HBV vaccination which was implemented as a national program starting in 1995. The aim of this study was to assess the period effect of the national HBV vaccination on liver cancer mortality in a young population. We compared age-specific mortality rates of liver cancer before and after the national vaccination program in the Korean population under the age of 20. To reduce year-to-year fluctuations in mortality, calendar years and age groups were divided into 4-year strata and the mortality rates were calculated for each stratum. Period effects of the national vaccination program were analyzed using age-period-cohort modeling. A total of 370 liver cancer mortality cases were identified during the period from 1991 to 2006. The period effect of the national vaccination program for the period 2002-2006 had a significantly reduced liver cancer mortality rate when compared to the period 1991-1994 when the national vaccination program was not implemented (RR 0.30, 95% CI 0.21 ~ 0.44). After implementation of the national vaccination program, HBV prevalence in Korean declined from 6~8% to 2~3%. This study demonstrates that the national vaccination program has contributed to the reduction of liver cancer mortality beyond just a natural decrease in Korean children and adolescents.