We present a case of suprarenal and infrarenal absence of the inferior vena cava, combined with hyperhomocysteinemia in a 39-year-old woman who presented with symptoms of deep venous thrombosis. The patient also had a homozygous mutation of C677T methylenetetrahydrofolate reductase. Deep vein thrombosis has a multifactorial etiology involving both genetic and acquired factors. Absence of the inferior vena cava is a rare congenital anomaly, but recently it was confirmed as an important risk factor for the development of deep vein thrombosis, especially in young persons. Hypercoagulability due to hyperhomocysteinemia with a tendency toward venous stasis, mediated by congenital absence of the inferior vena cava is thought to have caused deep vein thrombosis in our patient. To our knowledge, this association has not yet been reported. The clinical features and prognosis of the entity are discussed.