The detection of embolic sources in patients with atrial fibrillation (AF) is important to guide anticoagulant therapy. Two-dimensional transesophageal echocardiography (TEE) is the gold standard to study left atrial appendage (LAA) anatomy and morphology, despite some false-positive diagnosis. We hypothesized that real time 3D TEE (RT3DTEE) is superior to 2DTEE in detecting and/or excluding LAA thrombi. We studied 93 patients with non-valvular AF (60 males, age = 67.1 +/- 14.2 years) referred for electric cardioversion with transthoracic, 2DTEE and RT3DTEE. Before cardioversion, TTE allowed a confident measurement of emptying velocity of LAA (LAAeV) only in 59/93 patients (63%). On the contrary a good quality TEE LAAeV was obtained in all patients with 49/93 (53%) dysfunctional LAA (LAAeV < 40 cm/s). A subgroup of 5 patients (7.2% of the 69 effective cardioversion) presented a persistent dysfunction after cardioversion (with LAAeV values of < 40 cm/s on the TEE post-CV). TEE allowed to observe a bilobed shape in 45 patients (48.4%) and three lobes in 22 patients (23.7%). In addition, besides to several additional findings, 2DTEE managed to detect thrombi with certainty in 8/93 patients (8.6%). In other 5 cases with diagnostic doubts for thrombi with 2DTEE (5/93 patients: 5.4%), the addition of the RT3DTEE mode allowed to discriminate with certainty the presence of just pectinate muscles in 4 patients RT3DTEE in patients with AF at risk of embolism is feasible, accurate and showed an additional diagnostic capability in the differential diagnosis of selected cases with suspected LAA thrombi.