HBoV-2, a new parvovirus, has been identified in stool samples and suggested as one of etiologic agents of acute gastroenteritis. The purpose of this study was to investigate the prevalence of HBoV-2 in children hospitalized with gastroenteritis. We studied the viral etiologic agents of 358 children hospitalized with gastroenteritis by ELISA or RT-PCR. A single viral agent was detected in 43.3% of the study population and more than one viral agent was found in 7.2%. Norovirus (26.2%) and rotavirus (22.6%) were the most frequently detected viral agents. HBoV-2 and HBoV-1 were detected in 3.6% and 0.5%, respectively. Most of HBoV-2 positive samples were detected in November 2008 and in February 2009. Co-detection of HBoV-2 with other viral agents was 61.5% (8/13 patients). These findings suggest that HBoV-2 may be a possible etiologic agent in gastroenteritis, but further studies are needed to define its role due to high rate of co-infection.