Thrombophilia is caused by several genetic and acquired factors. Existence of more than one genetic factor may increase the risk of developing recurrent thrombotic events. Here, we present a case of a 48-year-old male with a known history of deep venous thrombosis and a known mutation in factor V Leiden combined with mild protein S deficiency, who presented with a painful swelling in the left leg. Moreover, the patient had a history of diabetes, dyslipidemia and obesity. Prothrombin time and platelet count were within the normal range. The international normalized ratio and activated partial thromboplastin time were 3.21 and 36.7 s, respectively. The Doppler study showed a thrombus in the saphenous vein, and complementary genetic screening investigations revealed heterozygous mutation for prothrombin (G20210A). A diagnosis of multifactorial genetic thrombophilia was established. The patient was treated with warfarin, which resulted in significant improvement in the follow-ups, and at the time of reporting this case, there were no clinical or biological signs of thrombosis. The presence of multiple hereditary and acquired thrombophilic factors is a rare clinical presentation that requires close monitoring, for which a lifelong anticoagulation therapy should be discussed based on the clinical response of the patient.