Background Human Bocavirus (HBoV) is considered to be responsible for lower respiratory tract infections in small children. Recent publications also reported the detection of HBoV in stool samples of gastroenteritis patients. Therefore HBoV might be associated with gastroenteritis cases. Objectives To investigate the prevalence and the causative role of HBoV in gastroenteritis outbreaks in day care facilities for children. Study design We examined 307 stool samples using a real time PCR protocol for HBoV load. Samples were collected from 48 independent outbreaks of gastroenteritis in day care facilities. Results HBoV was detected in 14/307 stool samples (4.6%). HBoV load in the samples was low and the 14 HBoV positive samples were distributed among 13 different outbreaks. Coinfections with Norovirus in single samples were frequent (57.1%), but no gastroenteritis outbreak could be associated with HBoV infection or coinfection. Conclusions This study indicates that HBoV is not a causative agent for gastroenteritis outbreaks.