BACKGROUND Achieving unobstructed blood flow from the systemic ventricle to the aorta is important during the Fontan procedure for complex cyanotic congenital heart disease when there is systemic ventricular outflow obstruction (SVOO). Because SVOO can progress after the Fontan procedure if there is morphologic obstruction, we have adopted a policy of relieving obstructions to systemic blood flow. METHODS Twenty-five patients were treated by the Fontan procedure with SVOO. Twenty-one patients had undergone prior pulmonary artery banding and 10 patients had undergone prior arch repair. Systemic ventricular outflow obstruction progressed in 5 patients after the Fontan procedure. Main diagnosis was single ventricle in 12, tricuspid atresia in 5, transposition of the great arteries in 4, double-outlet right ventricle in 3, and common atrioventricular canal in 1. Mean age at operation was 6.5 years (range 1 to 15 years) and the average preoperative pressure gradient across the ascending aorta and systemic ventricle was 29 mm Hg (range 0 to 100 mm Hg). The Damus-Kaye-Stansel procedure was performed in 18 patients (double-barrel anastomosis in 13, end to side anastomosis in 5), and subaortic resection or ventricular septal defect or bulboventricular foramen enlargement was performed in 7. Double-barrel anastomosis has been our first choice since 1994, if the pulmonary valve is intact. Follow-up has ranged from 4 months to 14 years (average 5.0 years). Twenty-three of the 25 patients have undergone recatheterization (average 21.4 months later). RESULTS No early deaths were found; one late death was reported of a patient with single right ventricle (4.0%). The postoperative average pressure gradient was 1.1 mm Hg (0 to 10 mm Hg), and the average right atrial pressure was 14 mm Hg (9 to 20 mm Hg). In all patients who underwent ventricular septal defect or bulboventricular foramen enlargement, regular sinus rhythm was maintained postoperatively. Regarding the Damus-Kaye-Stansel procedure, there was minimal progression of semilunar valve insufficiency except in 1 patient who underwent end-to-side anastomosis with moderate pulmonary regurgitation postoperatively. CONCLUSIONS The midterm results of the Fontan procedure with SVOO have been satisfactory. Because SVOO might progress after the Fontan procedure if there is morphologic obstruction, an appropriate strategy to relieve obstruction to systemic blood flow should therefore be performed concomitantly with the Fontan procedure.