The availability of three‐dimensional measuring techniques coupled to specific image processing methods opens new opportunities for the analysis of bone structure. In particular, synchrotron radiation microtomography may provide three‐dimensional images with spatial resolution as high as one micrometer. Moreover, the use of a monoenergetic synchrotron beam, which avoids beam‐hardening effects, allows quantitative measurements of the degree of mineralization in bone samples. Indeed, the reconstructed gray levels of tomographic images correspond directly to a map of the linear attenuation coefficient within the sample. Since the absorption depends on the amount of mineral content, we proposed a calibration method to evaluate the three‐dimensional distribution of the degree of mineralization within the sample. First a theoretical linear relationship modeling the linear attenuation coefficient as a function of the hydroxyapatite concentrations was derived. Then, an experimental validation on phantoms confirmed both the accuracy of the image processing tools and the experimental setup used. Finally, the analysis of the degree of mineralization in four iliac crest bone biopsy samples was reported. Our method was compared to the reference microradiography technique, currently used for this quantification in two dimensions. The concentration values of the degree of mineralization were found with both techniques in the range 0.5–1.6 g of mineral per cubic centimeter of bone, both in cortical and in trabecular region. The mean difference between the two techniques was around 4.7%, and was slightly higher in trabecular region than in cortical bone.