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Inadvertent tracheal tube misplacement and particularly endobronchial intubation are well-known complications of emergency endotracheal intubation (ETI) in pediatric trauma patients, which require repositioning of the tube to avoid impairment of gas exchange. The main aim of study was to identify the frequency of tube misplacement and associated factors of pediatric trauma patients who received ETI either by prehospital physician-staffed emergency medical service (EMS), or at emergency department (ED) admission to a single level-1 trauma center. Sixty-five patients (median age 14 years and median injury severity score 29) were included. Of these, 30 underwent helicopter EMS ETI, 29 ground EMS ETI, and 6 ED ETI. Seventeen cases (26%) of tracheal tube misplacement were recognized. After multivariable analysis, tracheal tube misplacement was independently negatively associated with body weight (OR 0.86; 95% CI, 0.76–0.99; p = 0.032) and helicopter EMS ETI (OR 0.20; 95% CI, 0.04–0.97; p = 0.036). Two of nineteen patients received tube thoracostomy due to endobronchial intubation. Mortality and length of stay were comparable in patients with misplaced tubes and correctly placed tubes. The results suggest that particularly small children require attention to avoid tracheal tube misplacement, which emphasizes the need for special training. Helicopter EMS physicians’ expertise might be beneficial in prehospital pediatric trauma patients requiring advanced airway management.