Left atrial appendage thrombus (LAAT) may be detected by transesophageal echocardiography (TOE) in patients with atrial fibrillation (AF) despite continuous anticoagulation therapy. We examined the factors predisposing to LAAT in patients treated with the anticoagulants dabigatran and rivaroxaban. We retrospectively evaluated 1,256 AF patients from three centres who underwent TOE before electrical cardioversion (n = 611, 51.4%) or catheter ablation (n = 645, 48.6%) from January 2013 to December 2019 and had been on at least three weeks of continuous dabigatran (n = 603, 48%) or rivaroxaban (n = 653, 52%) therapy. Preprocedural TOE diagnosed LAAT in 51 patients (4.1%), including 30 patients (5%) treated with dabigatran and 21 patients (3.2%) treated with rivaroxaban (p=0.1145). In multivariate logistic regression, predictors of LAAT in patients treated with dabigatran were non-paroxysmal AF (vs. paroxysmal AF) (OR = 6.2, p=0.015), heart failure (OR = 3.22, p=0.003), and a eGFR <60 ml/min/1.73 m2 (OR = 2.65, p=0.012); the predictors in patients treated with rivaroxaban were non-paroxysmal AF (vs. paroxysmal AF) (OR = 5.73, p=0.0221) and heart failure (OR = 3.19, p=0.116). In ROC analysis of the dabigatran group, the area under the curve (AUC) for the CHA2DS2-VASc-RAF score was significantly higher (0.78) than those for the CHADS2, CHA2DS2-VASc, and R2CHADS2 scores (0.67, 0.70, and 0.72, respectively). In the rivaroxaban group, the CHA2DS2-VASc-RAF score also performed significantly better (AUC of 0.77) than the CHADS2, CHA2DS2-VASc, and R2CHADS2 scores (AUC of 0.66, 0.64, and 0.67, respectively). The risk of LAAT was the same for patients in both treatment groups. In all patients, non-paroxysmal AF or heart failure, and in patients treated with dabigatran an eGFR <60 ml/min/1.73 m2, were independent predictors of LAAT. The new CHA2DS2-VASc-RAF scale had the highest predictive value for LAAT in the entire study population.