Introduction Autosomal dominant polycystic kidney disease is a common syndrome. Renal and hepatic cysts can cause discomfort, bleeding, rupture, infection, hypertension and a mass effect with compression of adjacent organs. Case presentation A 48-year-old man with polycystic kidney disease and hypertension presented to the emergency department for bilateral flank pain. An abdominal computed tomography scan with contrast showed a 7 cm heterogeneous process posteriorly and laterally to the right kidney. It appeared to be a renal cyst associated with bleeding and bilateral pulmonary artery filling defects, apparently due to pulmonary embolism. Cavography following inferior vena cava filter insertion did not show any deep vein thrombosis. Discussion and conclusion The pulmonary embolism was probably caused by extrinsic inferior vena cava compression by a liver cyst. Virchow’s triad of stasis, vessel damage and hypercoagulability probably resulted in a thrombus which moved on the right side to the pulmonary artery. LEARNING POINTS Autosomal dominant polycystic kidney disease is a common syndrome. Renal and hepatic cysts can compress adjacent organs. The mass effect of a large cyst on the right side compressed the inferior vena cava, resulting in Virchow’s triad of stasis, vessel damage and hypercoagulability, which can cause pulmonary embolism.