The absence of the inferior vena cava (IVC) is a rare abnormality reported in less than 1% of the population. The condition is usually the result of defects during embryogenesis. The collateral veins are enlarged with agenesis IVC, enabling blood transport to the superior vena cava. Although the alternate pathways enable venous drainage of the lower extremities, IVC agenesis (IVCA) may predispose to venous hypertension and complications, including thromboembolism. This report includes a case of a 35-year-old obese male who presented with deep vein thrombosis (DVT) in his left lower extremity (LLE) with no predisposing factors, which led to an incidental discovery of the inferior vena cava agenesis. Imaging showed thrombosis of the deep veins of the LLE, absence of the IVC, enlarged paralumbar veins, filling of the superior vena cava, and left renal atrophy. The patient responded to therapeutic heparin infusion, and catheter placement and thrombectomy were performed. The patient was discharged on the third day with medications and vascular follow-up. It is essential to recognize the complications of IVCA and its correlation with other findings, such as atrophy of the kidney. The agenesis of IVC is a highly under-recognized cause of DVT of the lower extremities in the young population without other risk factors. Hence, a complete diagnostic evaluation is necessary for this age group, including imaging for vascular anomalies, besides the thrombophilic screening.