A 7-month-old boy with heterotaxy syndrome had partial atrioventricular septal defect and interrupted inferior vena cava with hemiazygos continuation to a left superior vena cava. The left side of the common atrium receiving all the venous drainage was in connection with the left ventricle and the aorta. The small atrium and the proximity of the pulmonary and hepatic vein orifices precluded complete baffling. This report describes an intraatrial baffle repair of anomalous systemic venous return without hepatic venous drainage. This resulted in good oxygenation postoperatively, with oxygen saturation ranging from 93% to 98%.