BACKGROUND: In fall 2009, Children\'s Hospital of Michigan (CHM) instituted combined isolation precautions (contact and droplet isolation) for pediatric inpatients with upper respiratory infection (URI) symptoms to prevent health care-associated infection. METHODS: Pediatric patients with symptoms of URI had nasopharyngeal (NP) swab samples obtained prospectively between January and April and September and December 2010 for small volume polymerase chain reaction (SVPCR) array respiratory panel (RP) multiplex nucleic acid testing. NP swabs or nasal washes were obtained for viral culture and rapid antigen testing (RAT). RESULTS: Of 499 evaluable SVPCR array RP samples, 344 (69%) tested positive for at least 1 of the 21 tested organisms. The most commonly identified pathogen was rhinovirus/enterovirus (181/344 [53%]) for which no RAT exists at CHM. Of 344 positive specimens, 57 (17%) had at least 2 identified pathogens; 8 (2%) of these had 3. In 11% of patients, molecular testing detected pathogens or pathogen combinations requiring both contact and droplet precautions. CONCLUSION: SVPCR array RP testing detected respiratory pathogens in pediatric patients with URI at rates higher than that of RAT and viral culture. Because of the pathogens and pathogen combinations detected, the study findings suggest that combined contact and droplet isolation precautions may be warranted to prevent health care-associated infection in pediatric inpatients with URI. Further studies will be needed to confirm these results.