Hospital mortality in children who undergo stem cell transplant (SCT) is high. Early warning scores aim at identifying deteriorating patients and at preventing adverse outcomes. The bedside pediatric early warning system (BedsidePEWS) is a pediatric early warning score based on 7 clinical indicators, ranging from 0 (all indicators within normal ranges for age) to 26. The aim of this case-control study was to assess the performance of BedsidePEWS in identifying clinical deterioration events among children admitted to an SCT unit. Cases were defined as clinical deterioration events; controls were all the other patients hospitalized on the same ward at the time of case occurrence. BedsidePEWS was retrospectively measured at 4-hour intervals in cases and controls 24 hours before an event (T4-T24). We studied 19 cases and 80 controls. The score significantly increased in cases from a median of 4 at T24 to a median of 14 at T4. The proportion of correctly classified cases and controls was >90% since T8. The area under the curve receiver operating characteristic was 0.9. BedsidePEWS is an accurate screening tool to predict clinical deterioration in SCT patients.