The role of vertebrate blood coagulation is to rapidly prevent the loss of body fluids following vascular injury without compromising blood flow through either the uninjured or damaged vessels. To achieve this the coagulation network is initiated and regulated by a complex network of interactions that are under the control of both positive and negative feedback loops that result in controlled fibrin deposition and platelet activation only at the site of injury. Anticoagulant molecules play key roles in preventing inappropriate initiation of coagulation as well as down-regulating thrombin generation at the site of injury. Tissue factor pathway inhibitor (TFPI) inhibits the initiation complex, antithrombin (AT) inhibits the active serine proteases directly, whereas the activated protein C pathway inhibits coagulation by inactivating the cofactors V and VIII. In this review the structure and function of these anticoagulant molecules and their inhibitory complexes is discussed.