Ischemic stroke is the major complication of atrial fibrillation (AF) and only proven preventive therapy is oral anticoagulant therapy (OAC). Previous studies reported the presence of thrombus in the left atrium (LA) or left atrial appendage (LAA) despite anticoagulant therapy. We aim to investigate the predictors of LA/LAA thrombus in patients under OAC therapy and long-term clinical impact of thrombus. We prospectively enrolled consecutive patients with permanent AF under OAC therapy. Patients baseline characteristics were recorded. Transesophageal echocardiographic study performed after complete transthoracic echocardiographic study. 3-D evaluation of LAA was made using 3-D zoom mode and thrombus was defined when echo reflecting, mobile mass detected. Patients clinical outcomes were decided according to hospital records or via phone calls. Among 184 patients, 28 LAT were detected. Mean CHA2DS2-VASc score was significantly higher in patients with LAT in comparison to patients without LAT. CHA2DS2-VASc score (p: 0.001), left atrial volume (p: 0.001), left atrial flow velocity (p: 0.006) and left ventricular ejection fraction (p: 0.014) were independently associated with LAT. Among the parameters in CHA2DS2-VASc score, the previous history of stroke and age were independently related to LAT. After 12months of follow-up, patients with LAT had more ischemic stroke than patients without LAT (7.1% vs 4.4%, p: 0.001 respectively). Although oral anticoagulation is the default treatment strategy for prevention of LAT and thromboembolism in patients with non-valvular AF, LAT still can be detected especially in patients with a high CHA2DS2-VASc score. Furthermore, the presence of LAT is significantly associated with future ischemic stroke.