Objective To compare the rates of invasive bacterial infection (IBI) (bacterial pathogen in blood or cerebrospinal fluid) and urinary tract infection (UTI) in febrile infants between 42 and 90 days of age who had and had not been vaccinated in the previous 48 hours.

Design Observational study; secondary analysis of a prospective registry-based cohort study.

Setting Paediatric emergency department.

Patients Infants 42–90 days of age with fever without source seen between 2010 and 2021.

Main outcome measures Rates of IBI (bacterial pathogen in blood or cerebrospinal fluid) and UTI (urine culture obtained by an aseptic method yielding growth of ≥10 000 cfu/mL with associated leucocyturia).

Results We included 1522 infants, including 185 (12.2%) vaccinated in the previous 48 hours. Overall, 19 (1.25%) were diagnosed with an IBI and 282 (18.5%) with a UTI. No recently immunised infants were diagnosed with an IBI (vs 19, 1.4% of those not recently immunised, p=0.2). The UTI rate was higher in infants not recently immunised (20.1% vs 7.0%, p<0.01; OR: 3.3 (1.9–5.9)).

Conclusions Although the rate of UTI in recently immunised infants 42–90 days old with fever without a source is lower than in those not recently immunised, recommending screening for UTI seems appropriate. If the lower rate of IBI among recently immunised well-appearing infants is confirmed, the recommendation to systematically perform blood tests in these infants should be reconsidered.