OBJECTIVE. To characterize causes of fever in children presenting to a pediatric emergency department (ED). METHODS. One-year retrospective review of ED records. Inclusion criteria were 2 to 36 months of age with a documented temperature ≥ 39°C. Exclusion criteria were elopement, repeat visit, and underlying diagnosis with a predisposition to infection. Medical records were reviewed using a predefined, study-specific, data abstraction tool. Based on diagnosis and pathogen detection, visits were assigned to 3 groups, laboratory confirmed pathogen and focal or nonfocal diagnosis without confirmed pathogen. RESULTS. A total of 1091 visits met inclusion criteria. Fourteen percent had a pathogen detected, 56% had a focal diagnosis without a confirmed pathogen, and 30% had a nonfocal diagnosis without confirmed pathogen. CONCLUSIONS. In a cohort of febrile children 2 to 36 months of age, only 14% had a confirmed pathogen. New rapid viral diagnostic techniques may provide an opportunity to improve diagnostic certainty in young children presenting with fever.