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Argatroban keeps the platelets in your blood from coagulating (clotting) to prevent unwanted blood clots that can occur while receiving heparin Argatroban is used to treat or prevent blood clots in people who have thrombocytopenia (low levels of platelets in the blood) caused by using heparin. Argatroban is sometimes used in people who are undergoing a procedure called angioplasty (to open blocked arteries). Argatroban may also be used for purposes not listed in this medication guide.Argatroban is used to prevent the formation of clots that may occur while taking coagulant drugs such as heparin. It belongs to a class of drugs known as direct thrombin inhibitors, which work, as the name suggests, by inhibiting thrombin, a chief factor in the formation of clots. Common side effects associated with argatroban include nausea, diarrhea, headache and bleeding around the IV needle site.