In this work, analytical transmission electron microscopy (TEM) was used to study the nanostructure of mineralised ivory dentine, in order to gain a clearer understanding of the relationship between the organic (collagen fibrils) and inorganic (calcium phosphate apatite crystals) components. Thin sections prepared by both focused ion beam (FIB) milling and ultramicrotomy, in the longitudinal and transverse planes, were investigated using electron energy-loss spectroscopy (EELS) in a monochromated field-emission gun scanning TEM (FEI Titan 80-300 FEGSTEM). Both low- and core-loss spectroscopy were used in the investigation, and the signals from phosphorous, carbon, calcium, nitrogen and oxygen were studied in detail. A combination of HAADF (high-angle annular dark-field)-STEM imaging and EELS analysis was used for simultaneous acquisition of both spatial and spectral information pixel by pixel (spectrum imaging). Across the collagen D banding in longitudinal sections, the relative thickness of the bright bands was significantly higher than that of the dark bands. Core-loss spectroscopy showed that the bright bands were richer in apatite than the dark bands. However, no ELNES variation was observed across the D banding. In transverse sections, significant changes in the carbon edge fine structure were observed at the interface between the extra- and intra-fibrillar regions.