Cardiac surgery with cardiopulmonary bypass is routinely used in neonates who require early repair of congenital heart diseases. However, the bypass temperature and use of deep hypothermic circulatory arrest, the composition of the priming and the acceptable degree of hemodilution, the prophylactic use of antifibrinolytic agents and steroids, the choice of myocardial protection, the best PaO2, and even the pump flow, are still subjects of debate, despite major improvements in neonatal bypass over the last decade. Nevertheless, there are some techniques that have reached a near-consensus and are highly recommended in neonates: the use of minaturized bypass circuits to reduce blood product transfusions and inflammation, ultrafiltration, and the continuous monitoring of mixed venous and regional oxygen saturations to assess adequacy of perfusion. Nevertheless, surprisingly many different techniques may lead to the same results and mortality rate. As operative mortality rates have declined, the comparison endpoints between techniques have moved and focus on morbidity rates, extubation delay, ICU and hospital length of stay; in other words, the cost and (of course) the late functional outcome are certainly the new goals of neonatal cardiopulmonary bypass.