Pertussis may go unrecognized during respiratory syncytial virus (RSV) epidemics. Nosocomially transmitted pertussis can be severe in infants. Polymerase chain reaction (PCR) screening may identify infants with pertussis on admission, allowing for preemptive isolation. In a random sample, 1 (0.6%) of 166 children admitted to the hospital during RSV season were Bordetella pertussis PCR positive during a nonepidemic period. These data show that screening may not be useful when pertussis prevalence is low.