Hypercoagulability is a well-documented and prominent risk factor for venous thromboembolism. The role of thrombophilia in arterial thrombotic events is less well defined. A 52-year-old male patient with multiple atherogenic risk factors was admitted for non-healing pedal ulcer and absent distal pulses. Based on the clinical presentation, Doppler ultrasound and angiography findings, the patient underwent elective in situ bypass arterial reconstruction. The saphenous vein graft was of satisfactory quality and the procedure went routinely. Acute graft thrombosis on postoperative day 0 was recognized immediately and prompted an emergent surgical revision. No technical errors or anatomical/mechanical causes for failed reconstruction were found and the graft was successfully thrombectomized using a Fogarty balloon-catheter. Graft rethrombosis, however, ensued after several hours. Considering the absence of threatening limb ischemia and the idiopathic recurrent thrombosis, raising suspicion of prothrombotic state, conservative treatment was pursued. Postoperative thrombophilia testing proved positive for activated protein C resistance, mandating introduction of chronic oral anticoagulation. Six months later, the operated extremity is viable. Inexplicable vascular graft thrombosis, particularly if early and recurrent, should raise suspicion of underlying thrombophilia. If confirmed by laboratory testing, long-term secondary antithrombotic prophylaxis may be required.