Calcification within breast cancer is a diagnostically significant radiological feature that generally consists of hydroxylapatite. Samples from 30 cases of breast carcinoma with calcification were investigated using optical microscopy, energy-dispersive X-ray analysis, transmission-electron microscopy, Fourier-transform infrared spectroscopy, Raman spectroscopy, synchrotron radiation X-ray diffraction and X-ray fluorescence. Under optical microscopy, the calcifications were found to consist of either irregular aggregates with widths > 200 μm or spherical aggregates similar to psammoma bodies with an average diameter of 30 μm. Transmission-electron microscopy showed that short columnar or dumbbell-shaped crystals with widths of 10–15 nm and lengths of 20–50 nm were the most common morphology; spherical aggregates (~1 μm in diameter) with amorphous coatings of fibrous nanocrystals were also observed. Results indicated that hydroxylapatite was the dominant mineral phase in the calcifications, and both CO32– and cation substitutions (Na, Mg, Zn, Fe, Sr, Cu and Mn) were present in the hydroxylapatite structure. Fourier-transform infrared spectra show peaks at 872 and 880 cm–1 indicating that CO32– substituted both the OH– (A type) and PO43– (B type) sites of hydroxylapatite, making it an A and B mixed type. The ratio of B- to A-type substitution was estimated in the range of 1.1–18.7 from the ratio of peak intensities (I872/I880), accompanied with CO32– contents from 1.1% to 14.5%. Trace arsenic, detected in situ by synchrotron radiation X-ray fluorescence was found to be distributed uniformly in the calcifications in the form of AsO43– substituting for PO43–. It is therefore proposed that identifying these trace elements in breast cancer calcifications may be promising for future clinical diagnostics.