The prothrombotic and hemostatic-altering environment that characterizes cardiac surgery in general and cardiopulmonary bypass (CPB) in particular is unparalleled in medicine, causing, in an alarming number of patients, both thrombotic and hemorrhagic events. Fundamentally, the primary objective of anticoagulant therapy during CPB is to prevent thrombin generation and its attendant prothrombotic, proinflammatory, and vascular effects. Though anticoagulation with unfractionated heparin has been the standard of care for more than a half-century for patients undergoing cardiac surgery, inherent limitations, and an unfavorable safety profile will increasingly stimulate the investigation and development of more safe and effective therapies.