A 79-year-old woman with prosthetic valve endocarditis (PVE) on aortic position underwent re-aortic valve replacement. Although emergency operation was indicated due to huge vegetation over 20 mm in diameter attached to the prosthesis shown by preoperative transesophageal echocardiography, intraoperative transesophageal echocardiography showed disappearance of the vegetation. The prosthesis was carefully removed and replaced by a new bioprosthesis, though only small vegetation was observed on the removed prosthesis. Sudden blue toe 11 h after the operation and diminished pulse on right pedal artery suggested an acute arterial occlusion of a right lower extremity, requiring an emergency thrombectomy. Pathology diagnosed bacterial embolus with fresh thrombus that was considered apart from the prosthesis at the time of operation.