Calcium phosphates are used widely as orthopaedic implants and in nanocrystalline form to enable the transfer of genetic material into cells. Despite widespread use, little is known about their fate after they have crossed the cell membrane. Here we present a method of surface modification of silicon-substituted hydroxyapatite (SiHA) through a silane group, which enables the engraftment of a fluorescent dye to facilitate real-time biological tracking. Surface modification of the nanocrystal surface was undertaken using (3-mercaptopropyl)trimethoxysilane (MPTS), which presented a thiol for the further attachment of a fluorophore. Successful modification of the surface was demonstrated using zeta potential measurements and fluorescence microscopy and the number of thiol groups at the surface was quantified using Ellman's reagent. In vitro experiments using the fluorescently modified particles enabled the discrimination of the calcium phosphate particulate from other biological debris following internalisation by a population of MC3T3 (pre-osteoblast) cells and the particles were shown to maintain fluorescence for 24 hours without quenching. The successful modification of the surface of SiHA with thiol groups offers the tantalising possibility of the intracellular growth factor delivery.