Abstract: Objective To analyze pathogenic characteristics of hand,foot and mouth disease(HFMD)in Ji'nan city of Shandong province from 2009 through 2013 and to provide evidences for prevention and control of the disease.Methods Specimens including stool and pharynx swabs were collected from 3792 clinically-diagnosed cases of HFMD(including 138 severe cases)in Ji'nan city from 2009 through 2013 and epidemiological data on the cases were collected.Reverse transcription PCR(RT-PCR)analysis was used with universal primers within 5'untranslated region of enterovirus and VP1 region of coxsackievirus A16(CoxA16)and enterovirus 71(EV71)to assay the enteroviruses isolated from the HFMD cases.Statistical analysis of epidemiological data was conducted with SPSS 11.0.Results Among the 3792 specimens from the HFMD cases,the positive rate of enterovirus RNA was 74.97%(2843/3792);of the 2843 enterovirus RNA positive cases,1143(40.20%) were positive for EV71,955(33.59%) positive for CoxA16,737(25.92%) positive for other enteroviruses,and 8(0.28%) positive for both EV7l and CoxA16.The major pathogen of 138 severe HFMD cases was EV7l(86.36%).The majority of HFMD cases were less than 4 years old(82.15%) and the high-occurrence season of HFMD was from April to May of a year(31.70%).The positive rate of enteroviruses was not related with gender.The dominant prevalence of EV71 and CoxA16 alternated and the constituent ratio of the pathogens was significantly different between the years(χ²=116.38,P<0.05)in Ji'nan city during the 5-year period.Conclusion The major pathogens of HFMD epidemics were EV71 and CoxA16 and EV71 was a common pathogen of severe HFMD cases in Ji'nan city from 2009 through 2013.