In 1953, during the building restoration of San Michele church (Bono, Sardinia, 16th–19th Century), a high number of disarticulated skeletons were recovered. From a group of 412 hip bones, two of these, affected by several pathological lesions, were analysed. The two coxal bones can be referred to the same individual, an adult man. A multi-analytical study, started with the purpose of investigating the bone pathology, was extended to characterize the mineral components of a large representative set of bones from the same ossuary, all attributed to adult men who lived in the region four-two centuries ago. A quantitative ICP-AES analysis for Ca, Fe, Mg, Mn, Na, Pb and Zn was executed, and a chemometric investigation on the results was performed. This approach gave evidence of the effects of diagenesis, allowed some hypothesis of the incidence of the known dietary habits on bone composition, and completely differentiated the pathological bones from those of a normal population on the basis of the mineral composition. Moreover, porosity, crystallinity and FT-IR analysis were conducted on both non- and pathological sample.