We have previously shown that patients with a chromosome 22q11 microdeletion are at risk for prolonged respiratory failure after pulmonary artery reconstruction surgery compared with those with normal genotype. We sought to describe preexisting airway abnormalities in this patient population and examine relationships between airway abnormalities and outcomes. Single-center retrospective chart review from Society of Thoracic Surgery and Pediatric Cardiac Critical Care Consortium databases and the electronic medical record. Lucile Packard Children's Hospital at Stanford from September 2017 to February 2019. All patients undergoing pulmonary artery reconstruction surgery were considered for inclusion. We identified 127 patients meeting study inclusion criteria. Thirty-nine patients met specific criteria and underwent screening preoperative bronchoscopy including microdirect laryngoscopy and lower airway examination. Postoperative bronchoscopy was performed at the discretion of the intensive care team. Airway abnormalities were detected in 25/26 of children (96%) with a chromosome 22q11 deletion who underwent preoperative bronchoscopy. Upper and lower airway pathologies were found in 19/25 (73%) and 21/25 (81%) patients, respectively, and it was common for patients to have more than one abnormality. Presence of 22q11 deletion was associated with longer duration of mechanical ventilation (9.1 vs 4.3 d; p = 0.001), use of noninvasive positive pressure support (13 vs 6 d; p = 0.001), and longer hospital stays (30 vs 14 d; p = 0.002). These outcomes were worse when compared with patients with known airway abnormalities who did not have 22q11 deletion. Preexisting upper and lower airway pathologies are common in patients with a chromosome 22q11 deletion who undergo pulmonary artery reconstruction surgery. Despite similar postoperative hemodynamics and outcomes as their counterparts without 22q11 deletion, 22q11 deletion is associated with more postoperative respiratory complications not entirely explained by preexisting airway abnormalities.