We aimed to investigate the role of brain natriuretic peptide (BNP) levels and left ventricular (LV) filling pressures in thromboembolic risk in patients with non-valvular atrial fibrillation (AF). Among 327 patients with non-valvular AF, the ratio of peak early filling velocity to mitral annulus velocity (E/Ea) and N-terminal proBNP (NT-proBNP) was compared according to the presence of left atrial appendage (LAA) dysfunction [presence of spontaneous echo contrast (SEC)≥grade 3 and/or reduced LAA emptying flow velocity <20cm/s]. Compared to patients without LAA dysfunction, patients with LAA dysfunction presented with significantly higher CHADS2 scores (1.24±1.14 vs. 1.68±1.31, p=0.005), high-sensitivity C-reactive protein (0.36±1.18mg/dl vs. 0.66±1.32mg/dl, p=0.043), and NT-proBNP (765.3±2534.8pg/ml vs. 2266.9±6117.4pg/ml, p=0.002). Furthermore, patients with LAA dysfunction showed significantly higher left atrial volume index (LAVI, 25.1±10.9 vs. 43.1±22.1, p<0.001) and E/Ea (10.8±7.27 vs. 7.97±2.50mg/dl, p<0.001). Plasma logNT-proBNP levels were significantly correlated with the presence of SEC (r=0.276, p<0.001), LAA emptying flow velocity (r=-0.492, p<0.001), LAVI (r=0.405, p<0.001), and E/Ea (r=0.353, p<0.001). Binary logistic regression analysis showed that high NT-proBNP level >249.7pg/ml (odds ratio, OR 6.79, 95% confidence interval, CI 3.16-15.55, p<0.001) and E/Ea >10 (OR 4.41, 95% CI 2.39-8.15, p<0.001) were independent predictors of LAA dysfunction after adjustment of known thromboembolic risk factors. Elevated plasma NT-proBNP concentrations and LV filling pressures represented by LAA dysfunction may be reliable surrogate markers for predicting thromboembolic risk in patients with AF.