Left atrial thrombus (LAT) formation is associated with thromboembolic events. To investigate the incidence and associated factors of LAT in patients with atrial fibrillation (AF) who had been receiving anticoagulation therapy for more than 4weeks, and to develop a prediction model using clinical and echocardiographic features. Medical records of 1,122 patients with AF (mean age, 59.4 ± 11.0years, 58.3% male) who were on anticoagulation more than 4weeks and underwent transesophageal echocardiography (TEE) were evaluated. The main outcome was the presence of LAT on TEE. Warfarin and non-vitamin K oral anticoagulants were used in 74.4% and 25.6% of the patients at the time of examination, respectively. LAT was present in 60 patients (5.3%). Presence of LAT on TEE was associated with age ≥ 75years (odds ratio [OR] 2.13 [95% confidence interval, 0.94-4.58]), persistent/permanent AF (OR 2.61 [1.42-4.93]), CHA2DS2-VASc score ≥ 3 points (OR 1.91 [1.05-3.48]), left ventricular ejection fraction < 40% (OR 2.35 [1.07-4.81]), and severe left atrial enlargement (OR 3.52 [1.89-6.79]). The presence of moderate-to-severe mitral regurgitation was associated with a lower risk of LAT (OR 0.13 [0.04-0.34]). A scoring system composed of the aforementioned predictors showed excellent discrimination performance (area under the curve 0.791 [95% CI, 0.727-0.854]). LAT was present in a considerable number of patients who were already receiving anticoagulation therapy. A prediction model that combines clinical and echocardiographic predictors could be useful in distinguishing patients who require imaging evaluations before left atrial intervention.