A 41-year-old man with autosomal dominant polycystic kidney disease (ADPKD), who had multiple previous unprovoked thrombotic events and without a known coagulopathic disorder, presented with symptomatic extensive thrombus distal to the compression site of the left common iliac vein by a dominant cyst in the left inferior renal pole. This was managed with inferior vena cava filter insertion, left nephrectomy and warfarinization. Later, there was inferior vena cava compression by the right polycystic kidney, leading to elective right nephrectomy. Post-renal transplantation, he had further episodes of partial dialysis access stenosis and extensive thromboses in the left deep and right superficial venous systems of the lower limbs despite absence of extrinsic compression. This represents the first report of recurrent mass effect and thromboembolic events in ADPKD, both before and after nephrectomy and anticoagulation. The potential increased thromboembolic risks among patients with ADPKD warrant further investigation.