Some patients experience a left atrial thrombus (LAT) in spite of taking warfarin. We aimed to clarify the characteristics of patients with LAT during warfarin administration and investigated whether the CHADS2 or CHA2DS2-VASc scores are useful predictors of LAT. We studied 230 patients (169 males, age 65 ± 10 years) who underwent transesophageal echocardiography (TEE) prior to cardioversion or catheter ablation of atrial tachyarrhythmias between 2008 and 2012. All patients were taking oral warfarin. LAT was detected in 19 patients (8.3%) using TEE. LAT was significantly associated with the presence of hypertension (P = 0.0035), prior congestive heart failure (P < 0.0001), structural heart disease (P = 0.0012), persistent arrhythmias (P < 0.0001), the absence of SR during TEE (P = 0.0070), left ventricular ejection fraction (P < 0.0001), left atrial diameter (P = 0.0015), left ventricular dimension during end diastole (P = 0.0215), left ventricular hypertrophy (LVH; P < 0.0001), and the E/e' ratio (P = 0.0074). A multivariate analysis showed that LVH (P = 0.0065, OR 5.591, 95% CI 1.618–19.316) and persistent arrhythmia (P = 0.0364, OR 12.121, 95% CI 1.171–125.451) were independently associated with LAT. Moreover, the mean CHADS2 (2.3 ± 0.9 vs. 1.4 ± 1.2) and CHA2DS2-VASc scores (3.8 ± 1.2 vs. 2.8 ± 1.7) were higher in the patients with than without LAT. However, a multivariate analysis showed that the CHADS2/CHA2DS2-VASc scores did not associate with LAT. LVH and persistent arrhythmia may be useful for predicting LAT in patients with atrial tachyarrhythmias.