Background Emergency tracheal intubation during major trauma resuscitation may be associated with unrecognised endobronchial intubation. The risk factors and outcomes associated with this issue have not previously been fully defined. Methods We retrospectively analysed adult patients admitted directly from the scene to the ED of a single level 1 trauma centre, who received either prehospital or ED tracheal intubation prior to initial whole-body CT from January 2008 to December 2019. Our objectives were to describe tube-to- carina distances (TCDs) via CT and to assess the risk factors and outcomes (mortality, length of intensive care unit stay and mechanical ventilation) of patients with endobronchial intubation (TCD <0 cm) using a multivariable model. Results We included 616 patients and discovered 26 (4.2%) cases of endobronchial intubation identified on CT. Factors associated with an increased risk of endobronchial intubations were short body height (OR per 1 cm increase 0.89; 95% CI 0.84 to 0.94; p≤0.001), a high body mass index (OR 1.14; 95% CI 1.04 to 1.25; p=0.005) and ED intubation (OR 3.62; 95% CI 1.39 to 8.90; p=0.006). Eight of 26 cases underwent tube thoracostomy, four of whom had no evidence of underlying chest injury on CT. There was no statistically significant difference in mortality or length of stay although the absolute number of endobronchial intubations was small. Conclusions Short body height and high body mass index were associated with endobronchial intubation. Before considering tube thoracostomy in intubated major trauma patients suspected of pneumothorax, the possibility of unrecognised endobronchial intubation should be considered.