Abstract: Objective To investigate the pathogen spectrum and characteristics of diarrheal diseases among children under five and to provide the basis for prevention and control measures. Methods From February 2012 to January 2013, a total of 619 cases from 2 sentinel hospitals were collected for case survey. From them were collected stool specimens for detection of enteric pathogenic bacteria and virus nucleic acids. Results The virus detection rate was norovirus(11.95%), rotavirus(7.27%), enteric adenovirus(2.91%), saporovirus(1.45%) and astrovirus(0.97%). The bacteria detection rate was E. coli(5.65%),nontyphoidal salmonella (2.42%),campylobacter (0.81%), aeromonas hydrophila (0.65%),shigella(0.48%) and yersinia enterocolitica (0.32%). The virus detection rate was 27.70% from August to next March, which showed higher than that of other months(18.48%)(χ²=7.18,P<0.05). The bacteria detection rate was 15.34% from April to October, showing higher than the rate of other months(3.15%)(χ²=31.22,P<0.05). Conclusion Norovirus is the main pathogen for viral diarrheal diseases in children under five and E. coli is the main pathogen of bacterial diarrheal diseases. All study results suggested that summer and autumn should be as the focus time in prevention and control of bacterial diarrhea, while those of viral diarrhea should cover the whole year.