Human bocavirus (HBoV)-2, a new parvovirus, has been identified in stool samples and is suggested to be one of the etiologic agents of acute gastroenteritis (GE). The purpose of this study was to investigate the prevalence of HBoV-2 in children with GE. Stool samples were collected from 358 children hospitalized with GE. HBoV-2 was detected in 3.6% of the patients. HBoV-2 was co-detected with other viral agents in 53.8% of the patients. These findings suggest that HBoV-2 may be an etiologic agent in GE, but further studies are needed due to frequent co-detection with other enteric viruses.