At present, computer-assisted molecular modeling and virtual screening have become effective and widelyused tools for drug design. However, a prerequisite for design and synthesis of a therapeutic agent is determination of a correct target in the metabolic system, which should be either inhibited or stimulated. Solution of this extremely complicated problem can also be assisted by computational methods. This review discusses the use of mathematical models of blood coagulation and platelet-mediated primary hemostasis and thrombosis as cost-effective and time-saving tools in research, clinical practice, and development of new therapeutic agents and biomaterials. We focus on four aspects of their application: 1) efficient diagnostics, i.e. theoretical interpretation of diagnostic data, including sensitivity of various clotting assays to the changes in the coagulation system; 2) elucidation of mechanisms of coagulation disorders (e.g. hemophilias and thrombophilias); 3) exploration of mechanisms of action of therapeutic agents (e.g. recombinant activated factor VII) and planning rational therapeutic strategy; 4) development of biomaterials with non-thrombogenic properties in the design of artificial organs and implantable devices. Accumulation of experimental knowledge about the blood coagulation system and about platelets, combined with impressive increase of computational power, promises rapid development of this field.