Thirteen patients with single ventricle equivalents and subaortic stenosis underwent relief of the stenosis and subsequent Fontan operation. Nine patients, group 1, had the obstruction relieved at 3.6 +/- 1.6 years of age whenever the pressure gradient became apparent. Four patients, group 2, had the subaortic stenosis operated on at the neonatal period, 10.5 +/- 10 days old, before hemodynamic evidence of obstruction. Preoperative pressure gradient across the outflow tract was 44.2 +/- 4.7 mm Hg in group 1 versus 4.7 +/- 5 mm Hg in group 2 (p = 0.002). Ventricular muscle mass was 186% +/- 18% in group 1 versus 114% +/- 5% of normal in group 2 (p = 0.0001), and mass/volume ratio was 1.12 +/- 0.62 in group 1 versus 0.62 +/- 0.16 in group 2 (p = 0.003). Relief of subaortic stenosis was achieved by proximal pulmonary artery to ascending aorta or aortic arch anastomosis and by systemic to distal pulmonary artery shunt. There was no hospital mortality or complication related to the procedure. At evaluation before Fontan operation, 4.3 +/- 1.6 years after relief of subaortic stenosis in group 1 and 3.2 +/- 0.9 years in group 2, the pressure gradient across the ventricular outflow tract was 4 +/- 3 mm Hg in group 1 versus 3 +/- 2 mm Hg in group 2 (p = not significant), ventricular muscle mass was 184% +/- 31% in group 1 versus 114% +/- 5% of normal in group 2 (p = 0.003), and the mass/volume ratio was 1.17 +/- 0.2 in group 1 versus 0.62 +/- 0.2 in group 2 (p = 0.003). After Fontan operation, there were two perioperative deaths and two takedowns of Fontan operation in group 1. Postoperative mean right atrial pressure was 17.6 +/- 2.1 mm Hg in group 1 versus 11.3 +/- 1.7 mm Hg in group 2 (p = 0.01). Serious postoperative effusions were present in 4 of 5 patients (80%) in group 1 versus 0 of 4 patients (0%) in group 2. Data suggest that early relief of subaortic stenosis in single ventricle equivalents using the modified techniques described optimizes ventricular compliance, protects the pulmonary vascular bed, and improves the outcome after Fontan operation.