BACKGROUND The fenestration function is by allowing a right-to-left shunt resulting in an increased cardiac index, associated with mild arterial oxygen desaturation. Subsequent transcatheter fenestration closure can be performed after haemodynamic assessment. The purpose of this study was to compare the outcomes of extracardiac connection (EC) with or without fenestration. METHODS Ninety-five consecutive patients diagnosed with univentricular heart disease underwent EC using Gore-Tax conduits at the Department of Children's Heart Center, Justus-Liebig-University Giessen Germany from June 1996 to July 2007. According to EC with or without fenestration, the patients were assigned to two groups (group A with fenestration and group B without fenestration). Mortality, effusions, postoperative mean pulmonary artery pressure, postoperative oxygen saturation, postoperative thrombosis, postoperative neurological problems, and the postoperative loss of sinus rhythm were compared. In group A, 23 patients had fenestration closed interventionally after a mean time of 20-22 months. RESULTS Mortality and postoperative mean pulmonary artery pressure in group B (3 and (15.1 +/- 3.4) mmHg, respectively) were significantly higher than group A (0 and (13.2 +/- 2.8) mmHg, respectively). Postoperative oxygen saturation, postoperative thrombosis, postoperative neurological problems, and the postoperative loss of sinus rhythm did not differ between cohorts. CONCLUSIONS Fenestrating an extracardiac tunnel seems to improve acute postoperative mortality by rising cardiac output. The induced right-to-left shunt shows no morbidity postoperatively. If a stabilized chronic hemodynamic situation is achieved, an interventional closure of the fenestration can be performed to advance the arterial saturation and improve the exercise tolerance of the patients.