We describe a patient with a diagnosis of heterotaxia and independent drainage of the suprahepatic veins into the venous atrium who underwent total extracardiac cavopulmonary connection in which hepatic vein drainage remained directly into the atrium. In the immediate postoperative period she showed increasing cyanosis that suggested substantial right-to-left shunt. Surgical ligation of the suprahepatic veins resolved the complication effectively without signs of hepatic congestion or portal hypertension.