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Bicuspid aortic valve is often associated with lesions of the ascending aorta, which differ histologically from those in tricuspid valve patients. We undertook proteomic analyses to assess differences at the proteome level. Aortic samples were collected from 20 patients undergoing aortic valve and/or ascending aortic replacement; 9 had a bicuspid valve: 5 with aortic aneurysm (diameter > 50 mm) and 4 without dilation; 11 had a tricuspid valve: 6 with aortic aneurysm and 5 without dilation. Patients with histologically proven connective tissue disorders were excluded. Samples were dissected, solubilized, and subjected to 2-dimensional gel electrophoresis. Gel patterns showed an average of 580 protein spots in samples from bicuspid valve patients, and 564 spots in those with tricuspid valves. Comparative analysis revealed a correlation coefficient of 0.93 for protein expression in the bicuspid valve group compared to the tricuspid group. Three protein spots were significantly over-expressed and 4 were significantly down-regulated in the bicuspid group compared to the tricuspid group. The lowest correlation in protein expression was between non-dilated aortic tissues. These differences between aortic tissues of bicuspid and tricuspid valve patients suggest that mechanisms of aortic dilation might differ, at least in part, between such patients.