Twelve children were identified with subaortic stenosis after Fontan's operation. All had absent resting and isoproterenol-provoked pressure gradient before the Fontan procedure. Six had a univentricular heart of left ventricular morphology, three had a single ventricle of right ventricular morphology, one had tricuspid atresia with transposition of the great arteries, one had pulmonary atresia, intact ventricular septum, and hypoplastic right ventricle, and one had corrected transposition with hypoplastic systemic ventricle. The median interval between the Fontan operation and the recognition of subaortic stenosis was 2.5 years. Ten patients underwent surgical treatment after a prior Fontan operation: Five had myectomy and enlargement of ventricular septal defect with two operative deaths; two had placement of a valved conduit from the ventricular apex to the descending aorta, and both died postoperatively; two with single ventricle had subaortic myectomy, and one had enlargement of ventricular septal defect and pulmonary aortic connection. Complete heart block developed in only one patient. Postoperative testing with Doppler echocardiography with color flow imaging demonstrated good relief of subaortic stenosis. All six children who survived the operation are well 4 months to 4 years later. Subaortic stenosis is a progressive lesion that may develop after a Fontan operation. Its surgical treatment continues to carry a significant mortality. Myectomy and enlargement of ventricular septal defect achieve direct relief of the obstruction with minimal risk of heart block.