Acute gastroenteritis (AGE), which is one of the most common diseases worldwide, primarily occurs in infants and young children in both developed and developing countries. To investigate the prevalence of AGE in Korea, 6,788 stool specimens collected from hospitalized patients with AGE in Seoul, Korea from March 2004 to June 2007 were analyzed by enzyme immunoassay, reverse transcription-PCR, DNA sequencing and phylogenetic analysis. Enteric viruses and bacteria were detected in 2,955 (43.5%) and 1,389 (20.5%) specimens, respectively. Among the enteric viruses detected, rotavirus (19.7%) and norovirus (18.9%) were the predominant causative agents, followed by adenovirus (2.5%) and astrovirus (2.4%). Staphylococcus aureus was the most commonly observed bacteria (8.0~19.2%). The epidemic peaks of the enteric viruses were October to December for norovirus, January to May for rotavirus, and August to October for adenovirus. The seasonal activity of rotavirus was shifted from winter to late spring. However, astrovirus did not display seasonal activity in this study. Although viral AGE primarily occurred in patients younger than 5 years of age, the incidence of viral AGE in children aged 6 to 14 years was significant. The results of this study will contribute to the currently available epidemiological data and improve public health and hygiene via amelioration of diagnostic methods and longitudinal surveillance.