A case of an 18-year-old man with deep venous thrombosis of the lower limbs caused by hypoplasia of the inferior vena cava in combination with heterozygous factor V Leiden is presented. Both anomalies were found when the patient complained of venous claudication in both thighs. Inferior vena cava malformation is a rare condition and may predispose to the development of deep venous thrombosis. This patient was at an even higher risk for deep venous thrombosis as the inferior vena cava malformation was combined with a hypercoagulable state.