The incidence of airway obstruction in patients with complex CHD other than vascular rings and absent pulmonary valve syndrome is unknown. We reviewed pre-operative CT and clinical data of children with conotruncal abnormalities to assess for airway obstruction. Airway obstruction was common (41% of patients), often moderate to severe, of diverse aetiology, and most commonly associated with a right aortic arch. Patients with airway obstruction showed a trend towards a higher mortality rate. Patients with complex conotruncal abnormalities should be assessed for airway obstruction as it may help predict the need for additional interventions and assist with prognostication.