This prospective clinical and virological study of 2,060 otherwise healthy children aged <15 years of age (1,112 males; mean age ± SD, 3.46 ± 3.30 years) who attended the Emergency Department of Milan University's Institute of Pediatrics because of an acute disease excluding trauma during the winter season 2003–2004 was designed to compare the prevalence and clinical importance of human coronaviruses (HCoVs) in children. Real-time polymerase chain reaction (PCR) in nasopharyngeal aspirates revealed HCoV infection in 79 cases (3.8%): 33 HCoV-229E (1.6%), 13 HCoV-NL63 (0.6%), 11 HCoV-OC43 (0.5%), none HCoV-HKU1 genotype A, and 22 (1.1%) co-detections of a HCoV and another respiratory virus. The HCoVs were identified mainly in children with upper respiratory tract infection; there was no significant difference in clinical presentation between single HCoV infections and HCoV co-infections. Diagnostic methods were used in a limited number of patients, and the therapy prescribed and clinical outcomes were similar regardless of the viral strain. There were a few cases of other members of the households of HCoV-positive children falling ill during the 5–7 days following enrollment. These findings suggest that HCoV-229E and HCoV-OC43 have a limited clinical and socioeconomic impact on otherwise healthy children and their household contacts, and the HCoV-NL63 identified recently does not seem to be any different. The quantitative and qualitative role of HCoV-HKU1 genotype A is apparently very marginal. J. Med. Virol. 78:1609–1615, 2006. © 2006 Wiley-Liss, Inc.