We report a rare case of thrombosis in the inferior vena cava (IVC) due to enlarged cysts in autosomal dominant polycystic kidney disease. A 71-year-old woman visited our hospital with a complaint of rapid left lower extremity swelling. Computed tomography (CT) revealed massive thrombosis from the IVC to the bilateral common iliac vein. The extrinsic mechanical stress of renal cysts to the IVC seemed to have induced thrombosis in the vein that resulted in the cause of severe edema in the left lower extremity. Her renal cysts were percutaneously punctured for the relief of compression and she received injection of 99.5% ethanol for prevention against reaccumulation of cyst fluid after IVC filter had been positioned. The edema of her left lower extremity improved temporarily, however, follow-up CT two months after cyst puncture showed reaccumulation of the fluid. Therefore, excision of the responsible cyst wall by open surgery was carried out.