In heterotaxy syndrome, bronchopulmonary situs usually reflects atrial situs, resulting in either right (RAI) or left atrial isomerism (LAI). This study determines airway anomalies and its implications in patients with heterotaxy. This retrospective study included 223 patients with heterotaxy syndrome who received an integrated cardiac computed tomography evaluation. Patient database from 1995 to 2020 was reviewed. The patients were examined by a congenital heart disease team comprising pediatric cardiologists, radiologists, pulmonologists, and cardiovascular surgeons. Among the 223 patients, 189 (84.8%, M/F=1.66) had RAI and 29 had LAI (13.0%, M/F=0.71). Five patients had indeterminate isomerism (2.2%, M/F=1.5). Discordant bronchopulmonary and atrial situs occurred in 4% patients, while discordant bronchopulmonary, atrial, and splenic situs occurred in 23.2% patients. Lower airway stenosis was observed in 61 patients (27.4%), including 27.5%, 20.7%, and 60% RAI, LAI, and indeterminate isomerism patients, respectively (p=0.189). One patient had an intrinsic long segment lower tracheal stenosis and received slide tracheoplasty. Initial cardiac operation was performed in 213 patients. Higher surgical mortality occurred in patients with RAI (19.5% vs. none for LAI and indeterminate isomerism, p=0.038). In patients with RAI, lower airway anomaly/stenosis increased the duration of ventilator usage (p=0.030) but did not affect surgical mortality. Total anomalous pulmonary venous return to systemic veins and pulmonary venous stenosis were major surgical risk factors. Bronchopulmonary isomerism shares a similar isomeric pattern to cardiac atrial appendage. Lower airway anomalies/stenosis was common in patients with heterotaxy, resulting in prolonged ventilator therapy in patients with RAI.