Heparin, in various forms, is used in a variety of conditions including prophylaxis and treatment of thromboembolic disorders. Although the most common adverse effect related to the use of heparin is bleeding, heparin-induced thrombocytopenia (HIT) can also occur. Two types of HIT exist, HIT type I and type II. HIT type I is a mild and self-limiting disease in which the patient's platelet count may decrease slightly but will recover with continued treatment. This is in contrast to HIT type II, which may lead to potentially devastating complications. Patients with HIT type II are at increased risk for thromboembolic complications that are mediated through autoimmune reactions and therefore require anticoagulation with danaparoid or one of the direct thrombin inhibitors, including lepirudin, argatroban, or bivalirudin. Limited data are available on the use of these agents in special populations including patients who are pregnant or those undergoing procedures such as percutaneous coronary intervention, cardiopulmonary bypass and dialysis, and pregnancy. Future therapies may include the use of unfractionated heparin in combination with glycoprotein IIb/IIIa inhibitors during cardiopulmonary bypass.