The coagulation cascade can be pictured as a series of reactions in which a zymogen, a cofactor, and a converting enzyme interact to form a multimolecular complex on a natural surface. In each case, the four reactants must be present if the conversion of a zymogen to the corresponding serine protease is to take place at any significant rate. The principal natural anticoagulant systems that are able to exert damping effects on the various steps of the cascade are the heparin-antithrombin and protein C-thrombomodulin mechanisms that regulate the serine proteases and the cofactors or activated cofactors, respectively. Inherited thrombotic disorders associated with specific deficiencies of antithrombin, protein C, and protein S have been described. This review describes the biochemistry and physiology of these endogenous anticoagulant systems. The development of specific radioimmunoassay techniques for prothrombin activation fragment F1 + 2, fibrinopeptide A, and protein C activation peptide has allowed us to carry out studies of these endogenous regulatory mechanisms involved in thrombin generation in patients with deficiencies of antithrombin or protein C. This information is then used to construct a framework for understanding the pathophysiology of the prethrombotic and actively thrombotic states in humans with these clinical disorders.