For neonates with congenital heart disease presenting for cardiac surgery, anticoagulation for cardiopulmonary bypass (CPB) is necessary to prevent clotting as blood comes into contact with the unphysiologic surfaces of the extracorporeal circuit. This is achieved by the use of high dose heparin, which is used to inhibit the formation and activation of thrombin. Since neonatal prothrombin levels are low, rendering them unable to generate large amounts of thrombin, neonates with congenital heart disease requiring anticoagulation for CPB have historically been considered heparin sensitive (3). However, in a recent investigation conducted by this group, elevated baseline levels of thrombin production and activity were consistently found in neonates presenting for cardiac surgery (4). Additionally, despite routine heparin dosing, elevated markers of thrombin production were also found in these neonates during CPB when compared to their adult counterparts (4). Perhaps the assumption that neonates with congenital heart disease are similar to other healthy neonates in their impaired ability to generate thrombin is incorrect. Contact activation may occur preoperatively from the presence of indwelling umbilical catheters and central lines or from interventional manipulations in the cardiac catheterization lab and stimulate their coagulation systems to generate more thrombin than anticipated. Elevated thrombin levels in neonates presenting for cardiac surgery would consequently have important implications in determining the optimal heparin dose needed to provide adequate anticoagulation for CPB.