Human parechoviruses (HPeVs) are associated with gastroenteritis (GE), although their etiologic role is uncertain. The purpose of this study was to detect HPeVs in children with GE in Korea. A total of 348 stool samples that were negative for common enteric viruses were screened for HPeV using RT-PCR. Of the 348 stool samples, seven (2.0%) were positive for HPeV. Five Korean strains belonged to HPeV-1, and two strains belonged to HPeV-4. Four Korean HPeV-1 strains clustered with strain 7555312 and the other HPeV-1 strain clustered with the BNI-788St strain. Two HPeV-4 strains showed discordant phylogenic relationships in the 3D gene, suggesting that recombination had occurred. This is the first study reporting the detection of HPeVs in children with GE in Korea.