Continuous aspiration of subglottic secretions is effective in preventing ventilator-associated pneumonia, but it involves a risk of mucosal damage. The main objective of our study was to determine the incidence of airway complications related to continuous aspiration of subglottic secretions. In consecutive adult patients with continuous aspiration of subglottic secretions, we prospectively recorded clinical airway complications during the period after extubation. A multidetector computed tomography of the neck was performed during the period of 5 days following extubation to classify subglottic and tracheal lesions as mucosal thickening, cartilage thickening or deep ulceration. In the 86 patients included in the study, 6 (6.9%) had transient dyspnea, 7 (8.1%) had upper airway obstruction and 18 (20.9%) had dysphonia at extubation. Univariate analysis identified more attempts required for intubation (2.3 ± 1.1 vs. 1.2 ± 0.5; p = 0.001), difficult intubation (71.4 vs. 10.1%, p = 0.001) and Cormack score III-IV (71.4 vs. 8.8%; p < 0.001) as risk factors for having an upper airway obstruction at extubation. The incidence of failed extubation among patients after planned extubation was 18.9% and 11 patients (12.7%) required tracheostomy. A multidetector computed tomography was performed in 37 patients following extubation, and injuries were observed in 9 patients (24.3%) and classified as tracheal injuries in 2 patients (1 cartilage thickening and 1 mild stenosis with cartilage thickening) and as subglottic mucosal thickenings in 7 patients. The incidence of upper airway obstruction after extubation in patients with continuous aspiration of subglottic secretions was 8.1%, and the injuries observed by computed tomography were not severe and located mostly in subglottic space