A 42-year old man with thrombophilia (prothrombin gene mutation) required the insertion of an inferior vena cava filter because of recurrent gastrointestinal bleeding associated with oral anticoagulation. However, it penetrated through the retro-hepatic vena cava into the liver, being manifested by constant, blunt abdominal pain. Endovascular retrieval was considered of extreme risk, though a surgical approach was performed under cardiopulmonary bypass with deep hypothermic circulatory arrest. The patient has recovered uneventfully with complete symptom relief.