Complications of flexible bronchoscopy (FB) were prospectively evaluated during 1,328 diagnostic procedures in children, not in intensive care units. A total 92.8% of the procedures were performed in conscious patients under sedation and 7.2% under deep sedation. Supplementary oxygen was provided in approximately 80% of cases via endoscopic face mask (n=783) or nasal prongs (n=290). At least one complication was recorded in 91 cases (6.9%). Minor complications (n=69; 5.2%) included moderate and transient episodes of desaturation (n=15), isolated excessive coughing (n=22), excessive nausea reflex with coughing (n=20), transient laryngospasm (n=6) and epistaxis (n=6). Major complications (n=22; 1.7%) included oxygen desaturation to <90%, either isolated (n=10) or associated with laryngospasm (n=6), coughing (n=4), bronchospasm (n=1), and pneumothorax (n=1). Major complications involving oxygen desaturation were associated with age <2 yrs (13 of 529 versus 8 of 778) and laryngotracheal abnormalities (7 of 85 versus 14 of 1,222). The overall frequency of complications was similar in conscious (6.7%) but sedated patients and patients under deep (7.3%) sedation. However, the frequency of transient desaturation was significantly higher in children undergoing FB under deep sedation. Transient fever after bronchoalveolar lavage was observed in 52 of 277 cases (18.8%). Flexible bronchoscopy is a safe procedure with <2% major complications. Careful analysis of indications and clinical status for each patient, and proper anaesthesia and monitoring during the examination ensure that the procedure is successful, with a minimum of complications.