Long-term follow-up studies after intraatrial repair for complete transposition have shown postoperative morphologic and hemodynamic abnormalities in many patients which often require reevaluation and therapeutic intervention. The purpose of this study was to assess, using magnetic resonance imaging, the presence and extent of late postoperative complications in a large cohort of 44 patients undergoing repair with the Mustard procedure. Of these 34 had an intact ventricular septum with or without obstruction of the left ventricular outflow tract, while 10 had an associated ventricular septal defect. Transverse spin-echo and gradient-echo images were acquired of the entire heart from the diaphragm to the bifurcation of the pulmonary trunk. Additional oblique images were acquired for better visualization of venous connections. Abnormal findings were diagnosed by visual inspection of spin-echo and gradient-echo images, and diagnoses were compared to previous findings at cardiac catheterization. On magnetic resonance imaging, a baffle leak was seen in eight patients, two had pulmonary venous obstruction, four had obstruction at the caval veins, 23 had obstruction of the left ventricular outflow tract and 18 had tricuspid regurgitation. Cardiac catheterization showed a leak across the baffle in 16, pulmonary venous obstruction in two, obstruction at the caval veins in four, obstruction of the left ventricular outflow tract in nine, and tricuspid regurgitation in nine. We conclude that combined spin-echo and gradient-echo magnetic resonance imaging provides extensive noninvasive assessment of postoperative sequels and residuals in patients after the Mustard procedure for complete transposition.