Since its first identification in 2005, four species of human bocavirus (HBoV1-4) have been documented. HBoV1 and HBoV2 have been shown to be associated with respiratory tract illnesses, as well as with acute gastroenteritis (AGE), worldwide. However, reports on the prevalence, clinical significance, and molecular characteristics of the two most newly identified HBoV species, HBoV3 and HBoV4, are very limited. To detect and characterize HBoV3 and HBoV4 infections in children with AGE in China, stool specimens were collected from 366 children with AGE. HBoVs in these samples were amplified by nested polymerase chain reaction (PCR), sequenced, and phylogenetically analyzed. HBoVs were detected in 44 samples (12%), of which nine were HBoV1, 33 were HBoV2, and two were HBoV3. HBoV4 was not detected. Most HBoV-positive samples (35/44) were co-detected with other viral pathogens. Both HBoV3 samples were co-detected with rotavirus. Analysis of the HBoV3 (46-BJ07) genome sequence indicates that HBoV3 may be a recombinant derived from HBoV1 and HBoV2 or from HBoV1 and HBoV4. To our knowledge, this is the first report of HBoV3 in China. However, it is unclear whether HBoV3 is associated with AGE because of its low detection rate in AGE patients and its co-infection with other AGE-causing viruses.