Among thrombophilic risk factors for deep venous thrombosis (DVT), agenesis of the inferior vena cava (AIVC) is very rare, but it must be considered in specific settings. Here, we present the case of an 18-year-old woman who was admitted to the Emergency Department with swelling and pain of her left leg. Clinical examination and ultrasonography detected extensive proximal DVT of the left leg. After attempted mechanical thrombectomy failed, an abdominal CT scan was obtained, which demonstrated bilateral thrombosis of the iliac-femoral axis in the context of congenital AIVC. CONCLUSIONS Agenesis of the inferior vena cava is a rare risk factor for deep venous thrombosis.Agenesis of the inferior vena cava requires lifetime follow-up and treatment.Idiopathic deep venous thrombosis, especially in young patients, requires additional diagnostic investigation that considers congenital anomalies.