Abstract: Objective To analyze the epidemiological characteristics of hand foot and mouth disease (HFMD) in the mainland of China during 2008-2009. Methods The analysis was conducted on the incidence data of HFMD during 2008-2009 collected from the national disease reporting information system. Results A total of 1 664 480 cases of HFMD, including 14 977 severe cases and 479 deaths, were reported during this period. As time goes on, the disease spread gradually from central area to eastern, southern and northern areas. The reported case numbers declined in 2009 in the areas with high case numbers in 2008. Most cases were children aged5 years, accounting for 93.86% of the total. Among these cases, those in children age3 years accounted for 79.69%. The risks to become severe case or of death were greater in age group of 1-2 than in other groups. Totally 30 953 cases were laboratory confirmed, of which EV71 infections, Cox A16 infections and other enteric virus infections accounted for 50.81%, 28.27% and 20.93% respectively. Conclusion In recent 2 years, the incidence of HFMD and the incidences of severe cases and deaths caused by EV71 infection increased substantially in the mainland of China., which resulted in serious disease burden and public health problem. In the areas where EV71 is predominant, it is necessary to take effective intervention measures in early phase and strengthen the medical treatment of severe cases to reduce the case fatality. Further study should be conducted on the technical problems still existed in the prevention and control of HFMD.