In 90 patients with characteristics placing them at increased risk for a Fontan operation, a fenestration was created in the atrial baffle at the time of the Fontan repair. The rational was to allow a right to left shunt which would maintain cardiac output and limit right atrial pressure in the presence of conditions which limit pulmonary blood flow. Early mortality was 4/90 (4%), with an additional two patients having the Fontan repair taken down to a bidirectional cavopulmonary anastomosis. Postoperative right atrial pressures were low (average 13 mm Hg), as was the incidence of prolonged pleural effusions (13%). At short-term (average 13 months) follow-up, 77% of patients have had closure of the fenestration, and 92% are in New York Heart Association Class I. We conclude that baffle fenestration with subsequent transcatheter closure results in decreased mortality and morbidity among high risk patients undergoing a Fontan repair, and that the high functional level at short-term follow-up justifies continued aggressive management of such patients.