Operative mortality after repair of even the most complex congenital heart lesions has become rare. As such, the gaze of the surgical team has been diverted beyond that of early survival to focus on decreasing early and late morbidity. Important and concerning information is accumulating delineating the vulnerability of the neonatal brain to injury as the result of congenital heart disease and/or the techniques employed to correct the lesions. For many years the prevention of neurologic injury associated with congenital heart surgery has concentrated on "unraveling" the mysteries of the deleterious effects of intentional brain ischemia (in the form of deep hypothermic circulatory arrest) and developing methods to interrupt the pathway of irreversible injury. In the late 1990s, alternative perfusion techniques were developed to minimize or theoretically avoid the use of deep hypothermic circulatory arrest where it was once thought to be mandatory. Simultaneously, the rather routine use of noninvasive, real-time, neurologic monitoring has provided surgical teams the opportunity to intervene and prevent brain injury , thus eliminating the historic reliance on postoperative surrogate markers to define the presence of brain injury. It is yet undetermined whether these strategies will translate into improved short- and long-term neurologic outcome. Common to all surgical disciplines is a trend that as mortality decreases for a particular disease process, focus is adjusted, and refinements in treatment protocols are designed to minimize morbidity of the disease and its treatment. This natural refining process of a discipline's maturation is increasingly present in the field of congenital heart surgery.