Ventricular dysfunction, elevated pulmonary vascular resistance, and residual distal pulmonary artery distortion contribute to early mortality after a Fontan operation; they may be transient or reversible. A baffle fenestration, allowing right-to-left shunting, maintains cardiac output and limits right atrial pressure. A baffle fenestration was surgically created at the time of a modified Fontan repair in 20 consecutive patients. Risk factors included pulmonary artery pressure of 18 mm Hg or more, end-diastolic pressure of 12 mm Hg or more, valvar regurgitation, pulmonary artery distortion, pulmonary vascular resistance of 2 Woods' units or more, ventricular outflow obstruction, and complex anatomy. Nineteen of 20 patients survived. After the operation, mean arterial oxygen saturation was 86%, mean right atrial pressure was 15 mm Hg, and mean duration of pleural effusions was 6 days. Twelve of 19 survivors tolerated early test occlusion and had permanent transcatheter umbrella closure. Four patients failed early test occlusion, with a significant decrease in venous O2 saturation and a rise in central venous pressure, due to ventricular dysfunction, pulmonary artery distortion, or aortopulmonary collaterals. Three of four had successful late closure of the fenestration after correction of these abnormalities.