The blood coagulation system is a complicated cascade of reactions and feedback regulations that executes a rapid response to vascular injury, yet avoids occlusion of the vessel. There are several key components of this system in the regulation of blood clot propagation, such as antithrombin (AT), tissue factor pathway inhibitor (TFPI), thrombomodulin (TM) and protein C (PC), of which defect causes thromboembolic diseases. In recent years, targeted gene disruption technique by homologous recombination has been introduced to investigate the physiological roles of those natural anticoagulant molecules, not only in thrombogenesis but also in embyrogenesis. We have studied the natural anticoagulantion system in a decade, and recently established AT knockout mice as well as ryudocan (syndecan-4) knockout mice. Ryudocan is a cell surface heparan sulfate proteoglycan, which bears heparin-like glycosaminoglycan (heparan sulfate) cahins, originally cloned from rat microvascular endothelial cells. We have demonstrated that ryudocan deficiency impairs the control of coagulation in fetal vessels of the placenta in mice. We have also reported that complete antithrombin deficiency in mice results in embryonic lethality, with severe fibrin deposition in the myocardium and the liver, accompanied with extensive subcutaneous hemorrhage. In this presentation, recent advances in understanding roles of natural anticoagulant molecules through the researches of targeted gene-knockout mice, including our experiences in antithrombin deficient mice and ryudocan deficient mice, will be discussed.