This study reports the detection and the genetic characterization of HBoV, a new member in the Parvoviridae family. Among 177 fecal specimens collected from children with diarrhea younger than 5 years in Japan, 11 (6.2%) were positive for HBoV. Co-infection with other enteric viruses (norovirus and adenovirus) was found in nine (81.8%) pediatric patients, while monoinfection by HBoV alone was detected in two (18.2%) cases. Nucleotide sequence analysis of 11 Japanese HBoV strains revealed that seven HBoV sequences were most closely related to other HBoV 1 reference strains, while the other four strains were similar to HBoV 2A. These results indicated that HBoV was one of the viral agents found in stool specimens collected from children with acute gastroenteritis and HBoV 1 and 2A circulated in Japan between 2009 and 2010 epidemic season. J. Med. Virol. 84:901–905, 2012. © 2012 Wiley Periodicals, Inc.