Background: Detailed imaging of pulmonary artery (PA) anatomy and significant aortopulmonary collaterals (APCs) is crucial for surgical planning and follow-up in pts with complex congenital heart disease and pulmonary stenosis (PS) or atresia (PAtr). Because examination by echo is often technically limited, this study evaluated the utility of MRI as an alternate non-invasive imaging tool.Methods: Ten pts (median age 31 yrs, range 1-4 yrs) with poor echo windows underwent both cardiac catheterization (Cath) and MRI within a median of 3 mos (range 0.1-8 mos). Diagnoses included TOF/PAtr (n = 6), TOF/PS (n = 2), single ventricle with PAtr (n = 1) and heterotaxy syndrome with PS (n = 1). MRI was performed using ECG-gated spin echo and gradient echo sequences in standard and oblique imaging planes. Data were retrospectively evaluated using angiography at Cath as the reference standard.Results: MRI had 100% sensitivity and specificity for the diagnosis of main PA (n = 5) and branch PA hypoplasia or stenosis (n = 11), as well as discontinuous PAs (n = 3). There was complete agreement between MRI and Cath identification of significant APCs (n = 6). Main PA atresia was noted by MRI in 4 pts but was not definitively shown by Cath in any. MRI but not Cath precisely defined the distance between discontinuous PAs and their relationship to other mediastinal structures. MRI and Cath evaluation of aortopulmonary or Glenn shunt patency was concordant in all cases (n = 4).Conclusion: Cardiac MRI is a reliable non-invasive imaging modality to define PA and APC anatomy in pts with complex PS or PAtr.