Abstract: Objective To find out the epidemiological characteristics and incidence trend of Japanese encephalitis (JE) in Huainan, provide basis to develop prevention and control measures. Methods Descriptive epidemiological analysis was conducted on the epidemiological characteristics of JE over the years in Huainan. Results A total of 4444 JE cases were reported from 1952 to 2008, the incidence rate ranged from 0.14/lakh to 58.27/lakh, and the average annual incidence rate was 1.17/lakh. The incidence rate had decreased to＜1/lakh since 1995. The cases distributed in all the region of Huainan, but the incidence was higher in rural area than in urban area. The cases mainly occurred from June to September, but peaked during July-August with cases accounting for 93.18% of the total cases in a year Most cases (90.11%) were children less than 10 years old, of which the majority were scattered children. Many cases were the children in floating population. Conclusion The dramatic decrease of JE incidence since 1998 was considered to be related with the vaccination-key measure of the comprehensive prevention and control. It is still necessary to increase the JE vaccination coverage among the children in rural area and in floating population, and strengthen the disease surveillance, health education and anti-mosquito activity.