Congenital absence of the inferior vena cava (AIVC) has been reported as a risk factor of deep vein thrombosis (DVT) in young people. DVT is caused by an interaction between congenital coagulation abnormalities and acquired risk factors. We observed an 18-year-old patient with AIVC who developed recurrent deep vein thrombosis at the left leg. Molecular studies showed an etherozigousity for FV Leiden gene (G1691A) and a homozigousity for methylenetetraidrofolate reductase gene (C677T) in absence of folate and vitamin B12 deficiency. After the second DVT episode, the patient has been treated with heparin and oral anticoagulant without discontinuation.