Before and after surgical therapy, the anatomy of the pulmonary arteries in cyanotic congenital heart disease is often distorted. Pulmonary arterial anatomy was evaluated by magnetic resonance imaging (MRI) and angiography in 20 patients, ages 3 months to 20 years, with cyanotic heart disease associated with decreased pulmonary blood flow. Excellent correlation between MRI and angiographic estimates of pulmonary artery diameter was obtained (main pulmonary artery, r = 0.96; right pulmonary artery, r = 0.93; left pulmonary artery, r = 0.96). A similar excellent correlation (kappa = 0.83) was found in the assessment of the presence and severity of proximal pulmonary arterial stenoses. However, stenoses in the peripheral pulmonary arteries visualized with angiography were missed with MRI. MRI and angiography showed complete agreement in determining the patency of 11 surgical shunts. MRI did not demonstrate all of the systemic collateral vessels present with angiography, and the distal connections of collaterals were not detected with MRI. MRI is comparable to angiography in the evaluation of central pulmonary arterial anatomy over a wide range of ages. These findings suggest an important role for noninvasive MRI in the serial evaluation of pulmonary artery morphology in patients with cyanotic congenital heart disease before and after surgical repair.