Palliative and corrective operations for the treatment of cyanotic congenital heart disease frequently involve or potentially influence the size of the pulmonary arteries. Echocardiography and magnetic resonance imaging (MRI) are two noninvasive imaging techniques currently used to assess morphologic abnormalities of the pulmonary arteries. The purpose of this study was to evaluate the role of MRI in comparison with echocardiography for defining morphologic changes of the pulmonary arteries after congenital heart surgery. The MRI scans and echocardiograms of 33 patients with surgery involving or affecting the pulmonary arteries were compared. The pulmonary outflow tract, pulmonary confluence, right and left pulmonary arteries, and surgical shunts were separately evaluated. Cineangiography and surgical reports were used to confirm findings. MRI and echocardiography were equivalent for demonstrating abnormalities of the right ventricular outflow tract, main pulmonary artery, and a variety of pulmonary shunts. MRI was superior to echocardiography in demonstrating abnormalities of the right and left pulmonary arterial branches (p < 0.001). MRI is effective for monitoring pulmonary arterial status after surgery and is superior to echocardiography for the evaluation of the right and left pulmonary arteries.