Because patients with heparin-induced thrombocytopenia (HIT) have an extremely high frequency of developing thrombosis, treatment options other than heparin are essential. Prophylaxis against thrombosis should also be considered. The current American College of Chest Physicians guidelines for the treatment of acute heparin-induced thrombocytopenia and thrombosis syndrome (HITTS) include the use of danaparoid, lepirudin or argatroban, alone or in combination with warfarin. For documented clinical thrombosis associated with HIT, patients should be treated with a direct thrombin inhibitor at therapeutic activated partial thromboplastin time for 7 to 10 days. Warfarin should not be used during the acute phase of HIT, unless a thrombin inhibitor is being used simultaneously. Conversion to warfarin can be done when the acute phase of HIT has passed. Due to the high likelihood of cross-reactivity, the use of low molecular weight heparins in patients with HIT is not recommended. For prophylactic treatment of HIT patients, despite a lack of other indications for anticoagulation, a direct thrombin inhibitor can be initiated with a low level of anticoagulation until the thrombocytopenia resolves. This regimen is continued until laboratory evidence is provided that the HIT antibody is no longer detectable. HIT patients, in addition to needing anticoagulation to treat thrombosis, can require anticoagulation for non HIT-related events, such as for the treatment of myocardial infarction, unstable angina and long-term anticoagulation for heart valves or atrial fibrillation. For these situations, and if immediate anticoagulation is needed, the use of a direct thrombin inhibitor with switch-over to warfarin is a useful option. However, optimal dosing regimens have not been established in all cases.