Human cortical and trabecular bones are formed by individual osteons and bone packets, respectively, which are produced at different time points during the (re)modeling cycle by the coupled activity of bone cells. This leads to a heterogeneously mineralized bone material with a characteristic bone mineralization density distribution (BMDD) reflecting bone turnover, mineralization kinetics and average bone matrix age. In contrast to BMD, which is an estimate of the total amount of mineral in a scanned area of whole bone, BMDD describes the local mineral content of the bone matrix throughout the sample. Moreover, the mineral content of the bone matrix is playing a pivotal role in tuning its stiffness, strength and toughness. BMDD of healthy individuals shows a remarkably small biological variance suggesting the existence of an evolutionary optimum with respect to its biomechanical performance. Hence, any deviations from normal BMDD due to either disease and/or treatment might be of significant biological and clinical relevance. The development of appropriate methods to sensitively measure the BMDD in bone biopsies led to numerous applications of BMDD in the evaluation of diagnosis and treatment of bone diseases, while advancing the understanding of the bone material, concomitantly. For example, transiliacal bone biopsies of postmenopausal osteoporotic women were found to have mostly lower mineralization densities than normal, which were partly associated by an increase of bone turnover, but also caused by calcium and Vit-D deficiency. Antiresorptive therapy causes an increase of degree and homogeneity of mineralization within three years of treatment, while normal mineralization levels are not exceeded. In contrast, anabolic therapy like PTH decreases the degree and homogeneity of matrix mineralization, at least transiently. Osteogenesis imperfecta is generally associated with increased matrix mineralization contributing to the brittleness of bone in this disease, though bone turnover is usually increased suggesting an alteration in the mineralization kinetics. Furthermore, BMDD measurements combined with other scanning techniques like nanoindentation, Fourier transform infrared spectroscopy and small angle X-ray scattering can provide important insights into the structure–function relation of the bone matrix, and ultimately a better prediction of fracture risk in diseases, and after treatment.