Unexpected arterial oxygen desaturation occurred immediately after cardiopulmonary bypass in two children. Epicardial echocardiography demonstrated unroofing of the coronary sinus after a Fontan procedure in the first child and rapidly excluded this abnormality in the second, who had undergone closure of a sinus venosus defect and in whom there was also a left superior vena cava draining to the coronary sinus. Epicardial echocardiography determined management in both patients: Oversewing of the ostium of the coronary sinus was undertaken in the first case during an additional period of cardiopulmonary bypass. Oxygen saturation values improved with aggressive endotracheal lavage and aspiration of secretions in the second child. Epicardial echocardiography can identify unroofing of the coronary sinus (which may be difficult to diagnose by transesophageal echocardiography) and can identify or exclude this condition when unexpected arterial oxygen desaturation is present after cardiac surgery.