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Objective The objective of this study was to evaluate the feasibility of online real time three-dimensional transesophageal echocardiography (RT3DTEE) in the measurement of left atrial appendage (LAA) orifice size. We also analyzed the correlation between LAA ejection fraction (EF) and its peak empty velocity (PEV). Methods There were 91 subjects enrolled in this study, with 46 patients with AF and 45 individuals with sinus rhythm (SR). RT3DTEE was performed by four methods including iSlice and iCrop online and QLAB software 3DQ and GI-3DQ off-line which were used to measure LAA orifice area, long diameter, short diameter, depth in the largest LAA, and number of LAA lobes. These LAA parameters achieved by the four methods were compared, respectively. GI-3DQ off-line was used to measure LAA end-diastolic and end-systolic volumes to calculate EF of LAA. Two-dimensional (2D) TEE was applied to measure PEV of LAA. The correlation between EF and PEV was analyzed. Results There were no significant differences in all LAA parameters between any two RT3DTEE methods (All P > .05). There was a significant and positive correlation between PEV and EF (r = .423, P = .000). There were statistical differences in LAA EF and PEV between patients with AF and SR individuals (0.38 ± 0.12 vs 0.61 ± 0.07, 35.7 ± 12.1 vs 49.5 ± 10.0 cm/s, P = .000). Conclusion Using online RT3DTEE for measuring LAA orifice size is feasible, and online RT3DTEE is more convenient than offline RT3DTEE. EF is positively correlated with PEV. LAA function is significantly decreased in patients with AF.