Objectives: After a Fontan procedure, forward pulmonary blood flow is augmented during inspiration because of negative intrathoracic pressure. Total pulmonary blood flow is higher during inspiration. With hemidiaphragmatic paralysis, inspiratory augmentation of pulmonary flow is lost or diminished. The objective of this study was to compare early postoperative morbidity after the modified Fontan operation in patients with and without hemidiaphragmatic paralysis. Methods: A case-control analysis was performed comparing 10 patients with documented hemidiaphragmatic paralysis against 30 patients without paralysis who were matched for diagnosis, fenestration, and age. The following early postoperative outcomes were assessed: duration of ventilator support, duration of hospital stay, incidence of ascites, prolonged effusions, and readmission. Results: Preoperatively, there were no significant differences between the 2 groups. However, among the postoperative outcomes, the duration of hospital stay (25.4 ± 16.6 days vs 10.8 ± 6.3 days; P = .03), incidence of ascites (70% vs 3%; P < .001), prolonged pleural effusions (60% vs 13%; P =.007), and readmission (50% vs 7%; P = .007) were significantly greater in patients with hemidiaphragmatic paralysis than in those without hemidiaphragmatic paralysis. Conclusions: Hemidiaphragmatic paralysis after the modified Fontan operation is associated with an increase in early morbidity. Care should be taken to avoid injury to the phrenic nerve. Patients with prolonged effusions should be evaluated for hemidiaphragmatic paralysis.