Lanthanide-doped fluorescent hydroxyapatite/silica core–shell nanorods, 50–100 nm in length and 30 nm in width, were prepared by precipitation of calcium phosphate in the presence of Eu3+ and Y3+ ions at 60 °C, followed by hydrothermally enhanced crystallization, stabilization with poly(ethyleneimine), and reaction with tetraethyl orthosilicate. The fluorescence intensity of the Eu3+-doped hydroxyapatite nanorods was enhanced threefold by co-doping with Y3+ and doubled after hydrothermal treatment. Significantly, fluorescence quenching by water was reduced in the presence of the thin silica nanoshell to give a further doubling of the fluorescence intensity compared with lanthanide-doped hydroxyapatite nanoparticles prepared in the absence of tetraethyl orthosilicate. Our results suggest that a combination of lanthanide doping, controlled crystallization and core–shell fabrication is a promising route to the preparation of biocompatible calcium phosphate nanoparticles with enhanced fluorescence for potential use in biomedical applications.