The aim of the study was to examine the role of three-dimensional rotational angiography (3DRA) in assessing vascular and airway narrowing in children with a bidirectional cavopulmonary anastomosis (BCPA). The course of children with single ventricle physiology is often complicated by left pulmonary artery (LPA) and/or bronchial stenosis and may be related to aortic compression. 3DRA may be useful in evaluating this complex anatomy and possible mechanisms for the observed obstruction. Clinical data and imaging (2D angiography and 3DRA) of children with a BCPA were reviewed retrospectively. Measurements were taken at similar locations along the pulmonary arteries in both modalities and in the airways on 3DRA. Twenty-five children with a previous BCPA were assessed at mean age of 3.1 ± 2.0 years and weight of 13.6 ± 3.6 kg. Excellent correlation was found between 3DRA and 2D angiographic LPA measurements (r = 0.89, p < 0.0001). Twelve children had qualitative LPA stenosis on 3DRA, with a stenotic dimension of 6.6 ± 2.2 mm on 2D angiography and 6.8 ± 1.9 mm on 3DRA (r = 0.94, p < 0.0001). Ten cases with LPA stenosis also had bronchial stenosis (83 %). Qualitative airway assessment correlated with quantitative bronchial dimensions from 3DRA-derived tomographic images: Bronchial stenosis measured 4.4 ± 1.6 versus 5.9 ± 1.1 mm in those with a normal appearing bronchus (p = 0.009). Hybrid patients (initial palliation with bilateral pulmonary artery banding and arterial ductal stenting, n = 5) and all patients with a Damus–Kaye–Stansel (DKS) anastomosis (n = 9) were more likely to have LPA and left bronchial stenosis (OR 7.7, p = 0.04). 3DRA is a useful and accurate tool in assessment of LPA and airway narrowing after BCPA. Hybrid and DKS patients are more prone to LPA and bronchial stenosis, and 3DRA can provide insight into the mechanism.