We have performed multi-photon image reconstructions as well as polarization state analyses inside an artery wall affected by atherosclerosis to investigate the changes in collagen structure. Mice, either healthy or affected by spontaneous atherosclerosis, have been used for this purpose. A two-photon imaging system has been used to investigate atherosclerotic lesions in the ascending aorta of mice. Second harmonic imaging has been performed alternatively on healthy samples and on affected region. The reconstructed images show that the spatial distribution of the collagen network seems disorganized by the disease. The polarization state studies reveal however that the apparent disorganization of the collagen is related to its spatially diffuse distribution and that the internal structure of the collagen fibers is not affected by the disease. In addition, a theoretical simulation of the second harmonic polarization states shows that they are consistent with the known 3D structure of the collagen network.