Raman spectroscopy and imaging are known to be valuable tools for the analysis of bone, the determination of protein secondary structure, and the study of the composition of crystalline materials. We have utilized all of these attributes to examine how mechanical loading and the resulting deformation affects bone ultrastructure, addressing the hypothesis that bone spectra are altered, in both the organic and inorganic regions, in response to mechanical loading/deformation. Using a cylindrical indenter, we have permanently deformed bovine cortical bone specimens and investigated the ultrastructure in and around the deformed areas using hyperspectral Raman imaging coupled with multivariate analysis techniques. Indent morphology was further examined using scanning electron microscopy. Raman images taken at the edge of the indents show increases in the low-frequency component of the amide III band and high-frequency component of the amide I band. These changes are indicative of the rupture of collagen crosslinks due to shear forces exerted by the indenter passing through the bone. However, within the indent itself no evidence was seen of crosslink rupture, indicating that only compression of the organic matrix takes place in this region. We also present evidence of what is possibly a pressure-induced structural transformation occurring in the bone mineral within the indents, as indicated by the appearance of additional mineral factors in Raman image data from indented areas. These results give new insight into the mechanisms and causes of bone failure at the ultrastructural level.