Isolated cleft mitral valve (ICMV) is a rare entity not known to be related to pulmonary atresia with ventricular septal defect (PA-VSD). This report describes the use of cardiovascular magnetic resonance (CMR) imaging to diagnose ICMV in a patient with repaired PA-VSD who presented with incidental severe mitral regurgitation (MR) on follow-up echocardiography. An associated pulmonary varix secondary to the severe MR also was shown by CMR.