The modified Fontan procedure may be complicated by prolonged pleural drainage. Predisposing factors are not fully understood. This study examines perioperative variables associated with prolonged effusions. We examined the Fontan procedure in 41 patients. Mean age was 45 months (range, 9 to 113 months). Mean weight was 14.7 kg (range, 6.9 to 30.4 kg). Diagnoses included tricuspid atresia in 29 per cent, pulmonary atresia in 12 per cent, and double-outlet right ventricle in 12 per cent. Fontan revisions were excluded. The extracardiac Fontan was performed in 22 patients (54%) and the lateral tunnel (LT) in 18 (44%). Fenestration was performed in 56 per cent. Ten patients (24%) had prolonged pleural effusions. Mean chest tube output (24.2 vs 14.1 mL/kg/d, P < 0.01), days with chest tubes (10.2 vs 5.8 days, P < 0.01), and length of stay (20.8 vs 8.13 days, P < 0.01) were significantly greater in those with effusions. Preoperative mean pulmonary artery pressure was higher in patients with prolonged effusions (12.7 vs 9.90 mmHg, P = 0.001). No other factors were identified as risk factors. Prolonged pleural effusions (greater than 14 days) are common after the modified Fontan procedure. A higher preoperative mean pulmonary artery pressure may be predictive of these effusions. Fenestration, type of Fontan reconstruction, and size of extracardiac conduit did not predispose to postoperative effusions.