Abstract: Objective To understand the etiological characteristics of hand foot and mouth disease (HFMD) in children in Xuzhou during 2009-2010. Methods The throat swabs and anal swabs were collected from 511 suspected HFMD cases in outpatient and inpatient departments of Xuzhou Pediatrics Hospital or under routine surveillance to extract viral RNA and detect specific genes of EV, EV71 and Cox A16 by using real-time PCR. Results Of the 511 clinical samples from suspected HFMD cases, 288 were positive for enterovirus nucleic acid (56.36%). Of the 288 enterovirus positive samples, 202 were positive for EV71 nucleic acid, accounting for 70.14%, 55 were positive for Cox A16 nucleic acids, accounting for 19.10%. EV71 infection, Cox A16 infection and other enterovirus infection occurred in children aged5 years, but only EV71 infection occurred in children aged5 years. Conclusion HFMD mainly occurred in children aged 1-3 years in Xuzhou during 2009-2010, the major pathogen was EV71, followed by Cox A16.