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Fondaparinux is used to treat serious blood clots in the legs and/or lungs. It is usually used with another "blood thinner" medication (warfarin). If untreated, blood clots can travel to the lungs, heart, or brain, causing serious (possibly fatal) breathing problems, heart attack, or stroke. This drug may also be used to prevent blood clots after certain surgeries with an increased risk of blood clots (such as hip fracture, abdominal, knee/hip replacement). Fondaparinux is known as a "blood thinner" (anticoagulant). It is a drug similar to heparin that works by blocking certain natural substances in the blood that cause clotting.