AIM The mechanisms underlying the formation of abdominal aortic aneurysms have yet to be fully clarified. To identify key proteins generally involved in aneurysmal formation, proteomic profiles were compared between aneurysmal and non-aneurysmal regions of aortic walls from patients with abdominal aortic aneurysm. METHODS Aortic wall specimens were obtained from three patients with abdominal aortic aneurysm. Protein profiles of aortic wall samples including vascular media and adventitia were compared between aneurysmal and non-aneurysmal regions in each patient using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). Protein spots expressed differently between the two regions were identified by tandem mass spectrometry and verified by immunohistochemical investigations. RESULTS Image analysis of 2D-DIGE gels revealed 22 proteins spots expressed differently between aneurysmal and non-aneurysmal regions in all three patients. Among these, five protein spots that were up-regulated in the AA regions were successfully identified as complement component C4, fragments of the fibrinogen alpha or beta subunits, and actin. Immunohistochemical studies showed massive deposition of fibrin/fibrinogen or its fragments in the media, and complement C1q component, the molecule starting the classical complement pathway, in all three layers of the aneurysmal region. CONCLUSION Our proteomic and subsequent immunohistochemical studies revealed significant fibrinogenesis and fibrinolysis in the media, and activation of the classical complement pathway in all three layers of the aneurysmal region. These data promote understanding of mechanisms behind the formation of abdominal aortic aneurysms.