BACKGROUND: Hypothermic circulatory arrest is a widely used support technique during heart surgery in neonate and infants, but the difference in the effects of perfusion methods, total arrest versus continuous flow, on postoperative course has been controversial. METHODS: This study was retrospectively designed to examine the difference in effects of deep hypothermic circulatory arrest or continuous flow perfusion on postoperative courses including mortality and neurologic morbidity after arterial switch operation through chart review. We also examined the relationship between intraoperative data and postoperative outcomes. RESULTS: Of 72 patients, 44 patients (Total Circulatory Arrest (TCA) group; 26 patients had intact ventricular septum, 18 patients had ventricular septal defect) were treated with total arrest, and 28 patients (Continuous Perfusion Flow (CPF) group; 13 patients had intact ventricular septum, and 15 patients had ventricular septal defect) were treated with continuous flow. Hospital course, postoperative hemodynamic profiles, incidence of complications excluding neurology and mortality were not different between two groups. The incidence of neurologic abnormalities was higher two times in TCA group than in CPF group but was not significantly different. CONCLUSIONS: We could not confirm the differences in postoperative outcomes between both techniques, total circulatory arrest and continuous flow perfusion during arterial switch operation in neonates and infants.