Multiplex polymerase chain reaction (PCR) is used to detect respiratory viruses in pediatric emergency departments, but its indications and interpretation of results must still be clear. In the present study, we examined the effect of detecting a viral agent with multiplex PCR on patient management. Infants and toddlers, aged between 1-24 months, who presented to the pediatric emergency department with respiratory tract infection complaints and underwent multiplex-PCR between 1 January 2014 and 28 February 2020 were included in the study. Patients with at least one agent detected were considered as the study group, and patients without detection were considered as the control group. The same design was implemented only for patients with chronic diseases. A total of 1106 patients were recruited [median age: 6.7 months (range: 2.9-13.0 months)]. Seven hundred and eighty-nine in the study group and 317 in the control group. There were no significant differences between the groups in hospital admissions (study group: 271 admissions; control group: 89 admissions; p=0.055), length of hospital stay duration [mean ± standard deviation: 3.09±7.87 days (study group) and 2.6±7.79 days (control group); p=0.045], or antibiotic use [234 patients (study group) and 77 patients (control group); p=0.078]. When these variables were examined only for those with chronic diseases, there was no difference again. Although multiplex PCR is an ideal method with high sensitivity, specificity, and cost-effectiveness, the limits of its clinical application need to be clarified. We did not observe significant differences in the treatment of patients with detected viral agents.