The unusual clinical presentation, importance of imaging techniques and role of low molecular weight heparin are described for an initial treatment of thrombosis in inferior vena cava agenesis associated with heterozygous factor V Leiden. The patient, a 36-year-old woman, presented to the emergency room with sudden onset of back pain, swelling of the legs and thighs, and claudication while walking. Abdominal ultrasonography was immediately ordered. Anomalies in vascular blood flow were detected. Computed tomography was performed, and initially showed a complete absence of the infrarenal segment of inferior vena cava caudally to the origin of both renal veins. Treatment with enoxaparin (1 mg/kg twice per day) was started. The patient was discharged and returned to her activities of daily living two weeks after admission. This vascular abnormality is mostly incidentally diagnosed in adults and only a few cases are described as being associated with thrombophilia.