We performed a total repair for a 1-year-old boy with left isomerism, a common atrium, incomplete atrioventricular septal defect and hemiazygos continuation. The operation performed was intraatrial rerouting with a baffle and mitral repair. The postoperative course was uneventful. However, two and a half years after the total repair, the patient revealed obstruction of the systemic atrium constructed by the baffle and the left ventricular outflow tract. Reoperation to relieve these obstructions was successful.