Congenital heart disease occurs in roughly 0.7% of live-births. Approximately one-half of these defects are severe, requiring surgical correction or palliation. In a large percentage of such procedures in children, moderate or profound hypothermic cardiopulmonary bypass is employed. Because, nowadays, early correction of the defect rather than a palliative procedure is more frequently pursued, the surgeon, anesthesiologist, and perfusionist are called upon to manage younger and smaller children undergoing longer and more complex operations which necessitate longer times on bypass. Due to the particular underlying heart defect, the pathway of flow and viscosity of the blood are frequently different from those encountered in the adult with atherosclerotic coronary arterial or valvar heart disease. Thus, it is important for those caring for children undergoing cardiac surgery utilizing bypass to be well informed about its possible detrimental effects on the various organs. The purpose of this review will be to focus on the effects of bypass on flow to, and metabolism of, the organs and to highlight what is known with regard to these features in children rather than adults.