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Aim: Assessment of the value of left atrial deformation indices for prediction of left atrial appendage functioning patients with non-valvular atrial fibrillation. Method: The study included 250 patients with non-valvular atrial fibrillation and normal left atrial dimension. Trans-thoracic and trans-esophageal echocardiography were performed. Patients were divided into two groups; patients with LAA thrombus (group I) and patients without LAA thrombus (group II), a correlation between trans-esophageal and trans-thoracic data was analyzed. Results: Group I included110 patients (44%) and Group II 140 patients (56%). By TDI mean LA strain and strain rate were lower in group I (21.89 ± 7.75% vs 35.14 ± 9.28%; p < 0.001) and (1.15/sec, IQR 0.12–3/sec versus 2.1/sec, IQR 0.21–3/sec, p < 0.001) respectively. By speckle tracking PALS and strain rate were lower in group I (24.79 ± 7.78% vs 37.63 ± 8.64%; p value < 0.001) and (0.95 ± 0.32/sec. Vs 1.27 ± 0.32/sec p, value < 0.001) respectively. By TEE; group I had lower LAA EF (39.2 ± 13.55% vs 53.86 ± 12.7%); p < 0.001, and lower LAA emptying velocity (17.53 cm/s, IQR 9.54–77.4 vs 63.5 cm/s, IQR 7.89–86.4; p < 0.001). There was a good correlation between LA TDI and speckle tracking PALS and PALSR and LAA EF% and velocity p < 0.001. TDI and PALS and PALSR were found to be significant predictors for LAA thrombus (P < 0.05) with good sensitivity and specificity. Conclusion: Left atrium deformation indices are predictors of LAA thrombus or SEC in patients with non-valvular AF with accepted sensitivity and specificity.