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OBJECTIVES The objectives of this study were to evaluate the effect of ventricular morphology on perioperative outcomes during Fontan surgery. DESIGN Retrospective cohort study. SETTING Single standing, not-for-profit pediatric hospital. PARTICIPANTS A total of 72 patients who underwent Fontan surgery using cardiopulmonary bypass without aortic cross-clamp between January 1, 2009 and December 31, 2014. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS The patients were divided into 3 categories depending on their single-ventricle lesions: (1) LV group (n = 20): left dominant and hypoplastic right ventricle; (2) RV group (n = 37): right dominant and hypoplastic left ventricle; and (3) BV group (n = 15): biventricular or indeterminate dominance. Perioperative major adverse events were collected based on the Society of Thoracic Surgeons database. The need for perioperative allogeneic blood transfusions also was determined. The mean age was 3.3±1.7 years and the mean weight was 13.6±4.0 kg. All patients had extracardiac lateral tunnel or conduit Fontan procedures. Sixty-nine of the patients (96%) underwent tracheal extubation in the operating room. Anesthesia, surgery, and CPB times were 326±68, 239±73, and 70±41 minutes, respectively. Eleven patients (15%) required allogeneic blood products intraoperatively, while 30 patients (42%) required allogeneic blood products during the perioperative period. Length of cardiac intensive care unit stay and hospital stay (median [IQR]) were 1 [1,2] and 12 [9,18] days, respectively. There was no mortality and no significant differences between groups in major postoperative complications, anesthetic or surgical variables. CONCLUSIONS No difference in the immediate perioperative outcomes was noted based on ventricular morphology.