OBJECTIVE Children with Tetralogy of Fallot, Pulmonary Atresia, and Major Aortopulmonary Collaterals (TOF/PA/MAPCAs) undergoing unifocalization surgery are at risk for developing more postoperative respiratory complications than children undergoing other types of congenital heart surgery. Bronchoscopy is used in the perioperative period for diagnostic and therapeutic purposes. In this study, we describe bronchoscopic findings and identify factors associated with selection for bronchoscopy. METHODS Retrospective case-control. METHODS All patients with TOF/PA/MAPCAs who underwent unifocalization surgery from September 2005 through March 2016 were included. Patients who underwent bronchoscopy in the perioperative period were compared to a randomly selected cohort of 172 control patients who underwent unifocalization without bronchoscopy during the study period. RESULTS Forty-three children underwent perioperative bronchoscopy at a median of 9 days postoperatively. Baseline demographics were similar in bronchoscopy patients and controls. Patients who underwent bronchoscopy were more likely to have a chromosome 22q11 deletion and were more likely have undergone unifocalization surgery without intracardiac repair. These patients had a longer duration of mechanical ventilation, ICU duration, and length of hospitalization. Abnormalities were detected on bronchoscopy in 35 patients (81%), and 20 (35%) of bronchoscopy patients underwent a postoperative intervention related to abnormalities identified on bronchoscopy. CONCLUSIONS Bronchoscopy is a useful therapeutic and diagnostic instrument for children undergoing unifocalization surgery, capable of identifying abnormalities leading to an additional intervention in over one third of patients. Special attention should be given to children with a 22q11 deletion to expedite diagnosis and intervention for possible airway complications.