Epidemiological surveillance for Human Bocavirus (HBoV) was conducted on 105 fecal specimens from children with acute gastroenteritis in Bahia, Brazil. Among of a total 105 stool samples, 44 samples were positive for HBoV as detected by nested-PCR. Of the 44 positive samples, co-infections with other enteric viruses (Norovirus, Adenovirus, and Rotavirus) were found in 12 pediatric patients. Mixed infections among HBoV with Norovirus were frequently observed in this population. The phylogenetic analysis identified the presence of HBoV-1, and HBoV 2A species. This study shows that HBoV is another viral pathogen in the etiology of acute gastroenteritis in children in Bahia, Brazil.