Bone Material Strength index (BMSi) measured by Impact Microindentation is generally lower in subjects with fragility fractures independently of BMD values. We recently reported that in humans, BMSi values are strongly associated with material properties of subperiosteal mineralized bone surface (local mineral content, nanoporosity, pyridinoline content). In the present study we investigated the relationship of BMSi with material properties of the whole bone cortex, by analyzing thin sections of iliac crest biopsies (N = 12) from patients with different skeletal disorders and a wide range of BMD with or without fractures, by Fourier transform infrared imaging (FTIRI). The calculated parameters were:​ i) mineral and organic matrix content and their ratio (MM), ii) mineral maturity/crystallinity (MMC) and iii) the ratio of pyridinoline (Pyd) and divalent collagen cross-links (XLR). Results were expressed as images, which were converted to histogram distributions. For each histogram the characteristics recorded were:​ mean value, mode (most often occurring value), skewness, and kurtosis and their association with BMSi values was examined by correlation analysis. BMSi values were significantly correlated only with MM mean and mode values (r = 0.736, p = 0.0063, and r = 0.855, p = 0.0004, respectively), and with XLR mode values (r = −0.632, p = 0.0274). The results of the present study demonstrate that BMSi values are strongly associated with MM, a metric that corrects the mineral content for the organic matrix content, and may also depend on organic matrix quality. These and our previous observations strongly suggest that BMSi assesses material properties of cortical bone.