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BACKGROUND Molecular diagnostic methods enhance the sensitivity and broaden the spectrum of detectable respiratory viruses in febrile infants ≤90 days of life. We describe the occurrence of respiratory viruses in this population as well as the rates of serious bacterial infection (SBI) and respiratory viral co-infection with regard to viral characteristics. METHODS This was a prospective observational cohort study performed in the emergency department that included previously healthy febrile infants ≤90 days of life. Clinical and historical characteristics were documented and a respiratory nasal wash specimen was obtained from each patient. This sample was tested for 17 common respiratory pathogens and a chart review was conducted to ascertain if the infant was diagnosed with an SBI. RESULTS In a 12-month period, 67% of the 104 recruited febrile infants were positive for a respiratory virus. The most commonly detected viruses were rhinovirus, respiratory syncytial virus, enterovirus and influenza. The rate of respiratory viral and SBI co-infection was 9% overall and infants with either a systemic respiratory virus or negative viral testing were 3 times more likely to have an SBI than those with viruses typically restricted to the respiratory mucosa (95% CI: 1.1, 9.7). CONCLUSIONS Respiratory viruses are readily detectable via nasopharyngeal wash in febrile infants ≤90 days of life. With the enhanced sensitivity of molecular respiratory diagnostics, rates of co-infection of respiratory viruses and SBI may be higher than previously thought. Further investigation utilizing molecular diagnostics is needed to guide usage in febrile infants ≤90 days.