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An increased body mass index (BMI) is associated with a higher incidence of atrial fibrillation (AF) and a higher risk of thromboembolic complications in AF patients. The aim of this study was to investigate the effect of BMI on the risk of left atrial thrombi (LATs) in patients with nonvalvular AF/atrial flutter (AFl) (NV AF/AFl). Patients diagnosed with NVAF/AFl (between November 2018 and May 2020) were selected from the multicenter, prospective, observational Left Atrial Thrombus on Transesophageal Echocardiography (LATTEE) registry that included AF/AFl patients referred for cardioversion or ablation followed by transesophageal echocardiography. A total of 2816 AF/AFl patients (63.6% males; mean age 65.8 years; mean BMI 29.8 kg/m2) were included in the study. Two hundred and twenty-two of them (7.9%) had LATs. Compared with normal-weight patients, those with BMIs ≥ 25 kg/m2 more frequently presented clinical factors potentially provoking LATs, such as non-paroxysmal AF/AFl (p = 0.04), hypertension (p < 0.001), and diabetes (p < 0.001); had higher CHA2DS2 scores (p < 0.001); and had larger LA dimensions (LA diameter and LA area) (p < 0.001 for both parameters). On the other hand, they showed some features negatively related to thromboembolic risk; for example, they were younger (p < 0.001) and were more often male (p = 0.002). In addition, patients with abnormal BMIs were more likely to be smokers (p = 0.006) and to be treated with oral anticoagulants (p = 0.005). Despite these differences in the prevalence of thromboembolic risk factors, the incidence of LATs was not increased in patients with abnormal body weight (overweight and obese compared to normal-weight patients) in this large real-life cohort of AF/AFl patients. This is probably due to the balanced composition regarding the prevalence of positive and negative thromboembolic risk factors.