The evolution of cardiac surgery has led to increasing emphasis on complete repair of congenital heart defects early in life, nowadays increasingly performed in neonates or small infants. Good results have been achieved because of innovative techniques permitting reconstruction of normal anatomy, and restoration of normal physiology, before either the heart or the patient undergo deleterious adaptation to the congenitally abnormal physiology. Despite the ability surgically to correct complex defects in such small patients, limitations in outcome are sometimes encountered related to the systems necessary for repair. In particular, exposure to cardiopulmonary bypass may present the greatest challenge for these tiny patients.