Abstract The determination of the spatially resolved calcium distribution and concentration in bone is essential for the assessment of bone quality. It enables the diagnosis and elucidation of bone diseases, the course of bone remodelling and the assessment of bone quality at interfaces to implants. With time-of-flight secondary ion mass spectrometry (ToF-SIMS) the calcium distribution in bone cross sections is mapped semi-quantitatively with a lateral resolution of up to 1 μm. As standards for the calibration of the ToF-SIMS data calcium hydroxyapatite collagen scaffolds with different compositions were synthesized. The standards were characterised by loss of ignition, x-ray diffractometry (XRD) and x-ray photoelectron spectroscopy (XPS). The secondary ion count rate for calcium and the calcium content of the standards show a linear dependence. The obtained calibration curve is used for the quantification of the calcium content in the bone of rats. The calcium concentration within an animal model for osteoporosis induction is monitored. Exemplarily the calcium content of the bones was quantified by XPS for validation of the results. Furthermore a calcium mass image is compared with an XPS image to demonstrate the better lateral resolution of ToF-SIMS which advances the locally resolved quantification of the calcium content.