We report a case of infrarenal absence of the inferior vena cava (IVC) presenting as a major iliofemoral deep venous thrombosis in an adolescent. This is the first report of infrarenal IVC absence in which IVC thrombosis has been demonstrated in the perinatal period. We propose an association between perinatal IVC thrombosis and subsequent infrarenal IVC absence. In addition, the case demonstrates the importance of assessment for anatomical anomalies in patients presenting with apparently idiopathic deep venous thrombosis.