The changes of annual incidence rates were predicted for 7 cohorts of different ages either with or without vaccination. Cost-effectiveness ratio (CER) was estimated by the annual differences of HA incidence of the two scenarios at 15 years after inoculation, the medical costs and quality of life impact (QALY) for conditions related to the vaccination and disease. The estimated age specific HA incidence rates of the cohorts without vaccination fitted the observed age specific HA incidence rates quite well, indicating the correctness of our calculation models. Under the basecase assumptions, vaccination in general population would entail medical costs. The average CER was 153,277.6 Yuan/QALY, 11 times more than the average per-capita GNP in 1994. The basecase CERs varied from 113,369.3 Yuan/QALY in 10-19 years of age to 292,138.3 Yuan/QALY in age group 50-years. However, much better CERs are found when vaccination is directed toward a high risk population. In this case, widespread use of HAV vaccine in general population with intermediate epidemicity would not be cost-effective while it should be only focused on the high risk population. Sensitivity analysis showed that none of the basic variables might change this conclusion.