Pericardial tissue (bovine or porcine), chemically stabilized with glutaraldehyde (GA), is widely used in cardiovascular surgery in the form of bioprosthetic valves. GA reacts with tissue proteins and creates inter- and intra-molecular cross-links, resulting in improved durability. However, tissue calcification and mechanical damage are still unresolved problems. The purpose of this study was to examine the surface topography of normal human aortic valve and GA-stabilized porcine pericardium tissue in order to gain comparative insight into supramolecular structure of both tissues. The analysis was focused on morphologic evaluation of collagen constituents of the tissues. Atomic force microscopy working in the contact mode in air was employed in the study. Considerable diversity in the spatial orientation of collagen fibrils for the human aortic valve and pericardial tissue were observed. It was found that different forms of collagen fibril packing, i.e. dense and "in phase" or loose, could have an impact on the collagen D-banding pattern. Stabilization with GA introduced significant changes in the surface topography of collagen fibrils and in their spatial organization on the tissue surface. Strong disturbance in the fibril's D-spacing was observed. It was also suggested, that the observed structural changes at the supramolecular level might make an important contribution to the progressive damage and calcification of the tissue. The presented results demonstrate that the AFM method can be useful for non-destructive structural characterization of heart valves and bioprosthetic heart valve material.