Abstract: Objective To understand the epidemiological characteristics of hand foot and mouth disease (HFMD) in Tibet autonomous region during 2009-2013 and provide scientific evidence for the prevention and control of HFMD. Methods The incidence data of HFMD in Tibet during 2009-2013 was collected from national disease reporting information system to conduct descriptive epidemiological analysis, and the throat swabs, vesicle fluids and other specimens were collected from the cases for pathogen detection with real time RT-PCR. Results A total of 4471 HFMD cases, including 17 severe cases, were reported in Tibet during this period, no deaths were reported. The annual incidence of HFMD was 24.95/lakh. The annual incidence in 2010 (66.30/lakh) and in 2012 (42.12/lakh) were much higher than those in other years. The reported annual incidence was highest in Lhasa (90.79/lakh) and lowest in Chamdo (1.40/lakh). Two incidence peaks occurred during a year, one was during April-July, and another one was during September-October. More cases were reported in autumn peak. Most cases occurred in children aged ≤5 years old, accounting for 77.88%. Etiological surveillance indicated that EV71 was the major pathogen, accounting for 65.18%. Conclusion HFMD occurred in a yearly up and down pattern in Tibet during 2009-2013. Epidemiological characteristics of HFMD in Tibet were different from other provinces of China. Two incidence peaks of HFMD were observed, but more cases occurred in autumn peak than in spring peak. HFMD mainly occurred in children aged ≤5 years and most cases were caused by EV71. It is important to strengthen the prevention and control of HFMD among urban area living young children during the incidence peak period.