Parainfluenza type 3 virus (PIV-3), an important cause of acute lower respiratory illness in children, can be transmitted nosocomially. To differentiate between nosocomial transmission and community-acquired infection, a polymerase chain reaction-based sequencing assay was developed for the 5' noncoding region of the PIV-3 fusion protein gene and was applied to virus specimens from 10 children infected with PIV-3 during a hospital outbreak. Four strains of PIV-3 were identified among the 10 virus isolates. Six isolates, which appeared to belong to 1 strain, were obtained from a cluster of nosocomial cases in a pediatric intermediate care unit. In contrast, the remaining 4 isolates, which appeared to belong to 3 different strains, were obtained from children infected in the community or elsewhere in the hospital. These data indicate that multiple strains of PIV-3 can be found during a single epidemic and provide evidence that infections within the intermediate care unit were probably caused by transmission of 1 strain of virus within the unit rather than reintroduction of virus by new patients or staff.