Malformations of inferior vena cava (IVC) as agenesis are a rare congenital anomaly and cause of deep venous thrombosis (DVT) of lower limbs and should be investigated in young patients of unknown aetiology. Treatment with mechanical thrombectomy and thrombolysis can be considered in certain cases of DVT, promoting rapid clot removal, and has also been shown to be an effective treatment in acute DVT. We present a case of acute lower limb DVT associated with IVC agenesis in which Alteplase thrombolysis was used and thrombus aspiration with catheter bilaterally, with subsequent angioplasty of the common and external iliac, obtaining satisfactory results.