We compared the rates of detection of respiratory viruses by reverse-transcription polymerase chain reaction (RT-PCR) and by conventional viral culture in 668 combined nasal and throat samples from a prospective, multicenter, population-based study of acute respiratory tract infections among hospitalized children aged <5 years. RT-PCR increased the yield of viral identification by 2-fold, compared with that of culture alone. The increased sensitivity of viral detection by RT-PCR will yield better estimates of the population burden of viral respiratory infections.