question: During the COVID-19 pandemic, transesophageal echocardiography (TEE) for left atrial appendage thrombosis (LAAT) detection should be limited to situations of absolute necessity. We sought to identify the main conventional and functional echocardiographic parameters associated with LAAT on TEE in non-valvular atrial fibrillation (NVAF) patients planned for electrical cardioversion (ECV). This retrospective study included 125 consecutive NVAF patients (71.5±7.8 yrs, 75 males), who underwent TEE at our Institution between April 2016 and January 2020, to exclude LAAT before scheduled ECV. All patients underwent a transthoracic echocardiography (TTE) implemented with speckle tracking echocardiography (STE) analysis of left atrial (LA) strain and strain rate (SR) parameters. 28% of patients were diagnosed with LAAT, while 72% without LAAT. Compared to controls, patients with LAAT had significantly higher CHA(2)DS(2)-Vasc Score and average E/e’ ratio, and significantly lower left ventricular ejection fraction (LVEF). Moreover, LA-peak positive global atrial strain (GSA+) and LA-SR parameters were significantly reduced in patients with LAAT. Multivariate logistic regression revealed that, differently from CHA(2)DS(2)-Vasc Score, LVEF (OR 0.88, 95%CI 0.81–0.97, p = 0.01), average E/e’ ratio (OR 2.36, 95%CI 1.41–3.98, p = 0.001), and LA-GSA+ (OR 0.57, 95%CI 0.36-0-90, p = 0.01) were independently associated with LAAT. LA-GSA+ (optimal cut-off ≤ 9.1%, AUC 0.95) showed the highest diagnostic performance. Finally, a strong linear correlation of LA peak-to-peak SR with both LA appendage filling (r = 0.86) and emptying (r = 0.83) velocities was demonstrated. TTE implemented with STE analysis of LA mechanics improves thrombotic risk assessment of NVAF patients. SUPPLEMENTARY INFORMATION: The online version of this article (10.1007/s10554-020-02127-6) contains supplementary material, which is available to authorized users.