Objective To determine the prevalence of invasive bacterial infections (IBI, pathogenic bacteria in blood or cerebrospinal fluid) in infants less than 90 days old with fever without a source related to the presence or absence of fever on arrival to the emergency department (ED).

Design Prospective registry-based cohort study.

Setting Paediatric ED of a tertiary teaching hospital.

Patients We included infants less than 90 days old with a history of fever evaluated in the ED from 2003 to 2016.

Main outcomes and measures The prevalence of IBI in patients with a history of fever who were febrile and afebrile on arrival to the ED.

Results We included 2470 infants: 678 afebrile and 1792 febrile when evaluated in the ED. Fifty-nine (2.4%) were diagnosed with an IBI (bacteraemia 46, meningitis 7 and sepsis 6): 16 in the group of afebrile infants with a history of fever (2.4%, 95% CI 1.4 to 3.8 vs 43 in the febrile group, 2.4%, 95% CI 1.8 to 3.2). Of the 16 afebrile infants with a history of fever diagnosed with an IBI, 14 were well appearing. The rate of non-IBI (pathogenic bacteria in urine or stools) was similar in both groups (15.5% and 16.7%).

Conclusions The prevalence of IBI in infants ≤90 days with a history of fever is similar regardless of the presence of fever on the arrival at the ED. The approach to infants with a history of fever who are afebrile in the ED should not differ from that recommended for infants who are febrile in the ED.