Human bocaviruses (HBoVs) have been detected in human gastrointestinal infections worldwide. Although HBoV global prevalence and strains diversity have been reported, but epidemiological data from Taiwan is largely unavailable to date. A total of 110 fecal samples from stools of diarrheic children at a general hospital, Taiwan, obtained from August 2012 to July 2013, were analyzed by nested PCR targeting a partial fragment (576 bp) of HBoV VP1/VP2 gene, which revealed 4 positive fecal samples. Clinical symptoms of HBoV-associated acute gastroenteritis (AGE) were not different from those without HBoV. HBoV infection was seen only during the fall and winter seasons. This is the first description of HBoV infection in children with AGE in Taiwan. Systematic surveillance and evidence-based studies are required to determine the transmission pathways and spread of HBoV in Taiwan.