Objective: To study changes of ultrastructure of atrial endothelial cells during acute atrial fibrillation (AF) in canines, and explore the possible mechanism of AF left atrial thrombosis. Methods: A total of 16 healthy adult mongrel canines were randomly and equally divided into blank control group (only received thoracotomy without pacing) and rapid atrial pacing (RAP) group (established acute AF model). Myocardial tissue of left and right appendage were taken from two groups and received hematoxylin eosin (HE) staining, then myocardial cell morphological changes was observed under ordinary light microscope; morphological changes of appendage endothelial cells was observed under electron microscope. Results: (1) Paroxysmal AF was successfully induced in all canines of RAP group; (2) There were no significant difference in morphology of appendage and endocardial tissue under ordinary light microscope between two groups; 3. Under transmission electron microscope, endothelium cell of appendage tissue presented defect of different extent, and some shedding in RAP group; while endothelial cell layer was complete with absence of necrosis and shedding in blank control group. Compared with blank control group, there was significant rise in endothelial cell incompleteness (12.5% vs. 75.0%) in RAP group, P=0.041. Conclusion: When acute atrial fibrillation occurs, endothelial cell ultrastructure has already changed, which may be related to thrombosis adhered to wall during atrial fibrillation.