A 27-year-old man, who was diagnosed as having familial protein S deficiency, developed deep vein thrombosis complicated with pulmonary thromboembolism. Anticoagulant therapy and thrombolytic therapy were commenced after the insertion of a temporary inferior vena cava filter (t-IVC-f). However, on day 5 after t-IVC-f insertion, IVC venography showed filter thrombosis. On day 13, we made a venotomy and removed the captured thrombi and inserted a permanent IVC-f. After removal of the t-IVC-f via the right brachial vein, thrombi that had not been seen earlier appeared in the right atrium (RA). It was suspected that the thrombi around the catheter had likely been stripped off during the catheter removal procedure. After the abdomen was closed, an extra operation was immediately performed. Under complete extracorporeal circulation, the RA was opened and the all thrombi were removed. The patient recovered well and was discharged on the 21st postoperative day without any complications.