An 88-year-old woman complained of right quadrant abdominal pain and severe edema in both legs. She had a history of pulmonary embolism one month ago. Abdomen CT showed a huge hepatic cyst compressing the intrahepatic portion of the inferior vena cava (IVC). The venogram CT showed multifocal thrombosis in the iliocaval and both lower extremity veins. Percutaneous hepatic cyst drainage was carried out. Fluid analysis presented leukocytosis, which suggested an infected hepatic cyst. To prevent secondary pulmonary thromboembolism, an IVC filter was inserted before catheter drainage for the hepatic cyst. One week later, abdominal pain was relieved. Then, sclerotherapy for the remnant hepatic cyst was performed by ethanol. Follow-up CT showed an increased amount of thrombosis in the iliocaval and left calf vein, but the IVC filter prevented another thromboembolic event successfully. The patient started dabigatran, a new oral anticoagulant, and compression stockings were applied to both legs. After one month, no visible thrombosis in the pelvis or either extremity was detected in abdominal CT. This case suggests that a huge hepatic cyst, especially with infection, should be considered as a possible cause of deep vein thrombosis if no other risk factors for thromboembolism exist.