Filling defects of the left atrial appendage (LAA) on multidetector computed tomography (MDCT) are known to occur, not only due to LAA thrombi formation, but also due to the disturbance of blood flow in the LAA of patients with atrial fibrillation (AF). The purpose of this study was to evaluate the impact of the maintenance of sinus rhythm via ablation on the incidence of LAA filling defects on MDCT in patients with AF. A total of 459 consecutive patients were included in the present study. Prior to ablation, MDCT and transesophageal echocardiography (TEE) were performed. AF ablation was performed in patients without LAA thrombi confirmed on TEE. The LAA filling defects were evaluated on MDCT at 3 months after ablation. LAA filling defects were detected on MDCT in 51 patients (11.1 %), among whom the absence of LAA thrombi was confirmed in 42 patients using TEE. The LAA Doppler velocity in patients with LAA filling defects was lower than that of patients without filling defects (0.61 ± 0.19 vs. 0.47 ± 0.21 m/s; P < 0.0001). The sensitivity, specificity and negative predictive value of MDCT in the detection of thrombi were 100, 91 and 100 %, respectively. No LAA filling defects were observed on MDCT at 3 months after ablation in any of the patients, including the patients in whom filling defects were noted prior to the procedure. MDCT is useful for evaluating the presence of LAA thrombi and the blood flow of the LAA. The catheter ablation of AF not only suppresses AF, but also eliminates LAA filling defect on MDCT suggesting the improvement of LAA blood flow.