Background Bacteraemia is an important cause of morbidity and mortality in critically ill children. Our objective was to assess whether daily bathing in chlorhexidine gluconate (CHG) compared with standard bathing practices would reduce bacteraemia in critically ill children. Methods In an unmasked, cluster-randomised, two-period crossover trial, ten paediatric intensive-care units at five hospitals in the USA were randomly assigned a daily bathing routine for admitted patients older than 2 months, either standard bathing practices or using a cloth impregnated with 2% CHG, for a 6-month period. Units switched to the alternative bathing method for a second 6-month period. 6482 admissions were screened for eligibility. The primary outcome was an episode of bacteraemia. We did intention-to-treat (ITT) and per-protocol (PP) analyses. This study is registered with ClinicalTrials.gov (identifier NCT00549393). Findings 1521 admitted patients were excluded because their length of stay was less than 2 days, and 14 refused to participate. 4947 admissions were eligible for analysis. In the ITT population, a non-significant reduction in incidence of bacteraemia was noted with CHG bathing (3·52 per 1000 days, 95% CI 2·64-4·61) compared with standard practices (4·93 per 1000 days, 3·91-6·15; adjusted incidence rate ratio [aIRR] 0·71, 95% CI 0·42-1·20). In the PP population, incidence of bacteraemia was lower in patients receiving CHG bathing (3·28 per 1000 days, 2·27-4·58) compared with standard practices (4·93 per 1000 days, 3·91-6·15; aIRR 0·64, 0·42-0·98). No serious study-related adverse events were recorded, and the incidence of CHG-associated skin reactions was 1·2 per 1000 days (95% CI 0·60-2·02). Interpretation Critically ill children receiving daily CHG bathing had a lower incidence of bacteraemia compared with those receiving a standard bathing routine. Furthermore, the treatment was well tolerated. Funding Sage Products, US National Institutes of Health.