Breast calcifications, defined as calcium deposits within breast tissue, can arise from a vast number of aetiologies. Diffuse or scattered distribution is typically seen in benign entities. Approximately 95% of all Ductal carcinoma-in-situ, which represents 25–30% of all reported breast cancers are diagnosed because of mammographically detected microcalcifications. In this investigation dedicated to breast calcifications, we assessed at the micrometer scale their chemical nature through last generation micro-Fourier transform Infrared microspectroscopy and their structural characteristics through last generation field emission scanning electron microscopy. Several striking results have been obtained. Heavily mineralized deposits seem to be the result of the agglomeration of micrometer scale spherules and for the first time, we show that micrometer scale spherules display very different internal structure. Moreover, while Ca phosphate apatite and calcium oxalate dihydrate are the two chemical phases usually reported, we underline the presence of a third chemical phase namely amorphous carbonated calcium phosphate. In the case of duct carcinoma in situ (DCIS), the chemical composition as well as the carbonate level are very inhomogeneous even inside micrometer scale breast calcifications. Moreover, for some samples related to DCIS, special features at the micrometer scale seem to be related to this pathology because they were not found for the other pathologies.