The development of molecular methods such as PCR has made viral diagnostics widely available, allowing the identification of new viruses and the re-evaluation of the role of old viruses in respiratory infections in children. Respiratory syncytial virus (RSV) accounts for over 50% of wheezing episodes in infants below 12 months of age, whereas rhinoviruses (RVs) and other picornaviruses account for over 50% of wheezing episodes after 12 months of age. Human metapneumovirus accounts for 5–10% of wheezing episodes in infants. The recently identified human bocavirus is often, in up to 30% of the cases, involved with respiratory infections in children below 3 years of age, but the definite role of the virus in early-life wheezing is unresolved. Subsequent wheezing at 1–3 years of age is more common after RV-associated wheezing than after RSV-associated wheezing, and RV-associated wheezing may even be the first sign of childhood asthma. Respective follow-up data are not available for other viruses. The properties of viruses, the genetically regulated host responses and their interactions modify the clinical presentation, severity and outcome of respiratory infections in children.