Atrial fibrillation (AF) is the most common form of arrhythmia encountered in clinical practice, and contributes to cardiovascular morbidity and mortality. Despite significant advances in the understanding of the mechanisms associated with AF, the number of effective biomarkers and viable therapeutic targets remains relatively limited. In this study, 2-DE and MS/MS analysis was used to identify differentially expressed proteins in human atrial appendage tissues from patients with AF (n=4) compared to controls with sinus rhythm (SR; n=5). All subjects had rheumatic heart disease. Following 2-DE analysis, Coomassie Brilliant Blue staining and MS/MS identification, a total of 19 protein spots were found to be differentially expressed between the AF and SR groups. By cluster and metabolic/signaling pathway analysis, these proteins were divided into three major groups: proteins involved in the cytoskeleton and myofilament, energy metabolism associated proteins, and proteins associated with oxidative stress. The proteins identified in this study may enable a better understanding of the molecular mechanisms of AF, and may provide useful biomarkers and novel targets for drug development.