The left atrial appendage (LAA) represents one of the major sources of cardiac thrombi responsible for embolic stroke in patients with atrial fibrillation (AF). The aim of the present study was to evaluate LAA structure and functions by transesophageal echocardiography (TEE) in patients with AF to investigate the possible association between the different LAA morphologies and the patients’ history of ischemic cerebral stroke. We included 50 patients with non-valvular AF (29 chronic, 21 paroxysmal), 24 patients (13 men) without stroke; and 26 patients (9 men) with a history of ischemic stroke. All patients underwent TEE evaluation of LAA morphology and functions. Compared to patients without stroke, patients with ischemic stroke had significantly higher CHADS2 scores (4.19 ± 0.89 versus 1.67 ± 1.13; P < 0.001) and C-reactive protein levels (8.3 ± 1.6 versus 7.6 ± 0.83 mg/L; P = 0.023), and lower peak filling (21.7 ± 11.3 versus 31.2 ± 9.5 cm/second; P = 0.033) and emptying (22.2 ± 9.7 versus 33.4 ± 13.4 cm/second, P = 0.030) velocities. Triangular LAA morphology had a higher prevalence in patients with stroke (36% versus 12% in non-stroke group); and in half of them an LAA thrombus was present. LAA thrombi were detected in 9 patients (18%) with stroke and in 5 patients (10%) without stroke. On multivariate logistic regression analysis, age (OR = 1.202 [1.042–1.585]; P = 0.041), LAA orifice diameter (OR = 1.275 [1.102–1.748]; P = 0.028), and triangular LAA morphology (OR = 4.53 [1.629–8.381]; P = 0.011) were significantly and independently associated with ischemic stroke in AF patients. LAA morphology evaluated by TEE may be useful for predicting ischemic cerebral stroke in patients with non-valvular AF, especially in those with a low CHADS2 score.