- Heparin is a naturally occurring anticoagulant drug that combines with anti-thrombin III to inhibit many steps of the coagulation pathway. Clinically, heparin is used in small doses to prevent venous thrombosis and pulmonary embolism; in large doses, it is the treatment of choice in acute venous thromboembolism. Heparin also is used to treat some acute arterial thromboembolic episodes. Heparin may be given by intermittent intravenous injection or continuous intravenous infusion, usually in doses of approximately 30,000 units per day. Hemorrhage, the main side effect of heparin, appears to be less frequent when therapeutic doses are given by continuous intravenous infusion rather than by intermittent intravenous injection.