Venous thromboembolism (VTE) represents the formation of a blood clot in one of the deep veins of human body. The significant morbidity and mortality rates associated with VTE have spurred increasing investigations seeking to identify causative factors for this complex condition. While the most frequent causes of an inherited hypercoagulable state are the Factor V Leiden mutation and the prothrombin gene mutation, polymerase chain reaction (PCR) analysis has helped to identify other rare causes of inherited VTE. We report a case of a recurrent deep venous thrombosis in an end-stage renal disease patient. All laboratory tests for hypercoagulable states were normal. However, PCR analysis detected a rare polymorphism of prothrombin gene mutation at position C20209T, instead of G20210A. The patient was treated successfully with a high dose of warfarin to maintain adequate anti-coagulation during the 2-year follow-up.