Heparin-induced thrombocytopenia (HIT) with thrombosis is the most severe side effect of heparin administration. HIT patients may die or have permanent sequelae, such as a stroke or limb amputation. Contaminated heparin is associated with anaphylactic reactions and deaths by activating the contact system. It is also associated with high incidence of HIT via a yet unknown mechanism. This chapter shows that: (1) the contact system can be activated by a variety of unrelated molecules; (2) kallikrein directly cuts prothrombin to generate functional thrombin through contact system activation; and (3) while heparin contaminants, oversulfated heparin by-product (OS-HB), induce thrombin generation in both normal and HIT patient plasmas through contact system activation, authentic heparin induces thrombin activities only in HIT patient plasmas containing autoantibodies against protein/heparin complex. These data suggest that the negatively charged IgG/protein/heparin or OS-HB complex activate the contact system and produce thrombin in human plasma and thrombin partially activates the platelets allowing subsequent platelet activation through IgG/Fc receptor II signaling. The newly discovered mechanism of heparin-induced thrombin activity could explain the increased incidence of HIT in patients exposed to contaminated heparin. Furthermore, the assays used in these studies would be valuable for HIT diagnosis, prevention, and treatment.