Diatomite is a natural fossil material of sedimentary origin, constituted by fragments of diatom siliceous skeletons. In this work, the properties of diatomite nanoparticles as potential system for the drug delivery in cancer cells are exploited. A purification procedure, based on treatments in strong acid solutions, is used to remove inorganic and organic impurities from diatomite and to make them a safe material for medical applications. Morphology and composition of diatomite nanoparticles are investigated by SEM equipped by energy dispersive X-ray spectroscopy, FTIR analysis and photoluminescence measurements. Nanometric porous particles (average size lower than 350 nm) are obtained by mechanical crushing, sonication, and filtering of micrometric frustules. Moreover, diatomite nanoparticles are modified by a proper biochemical functionalization of surface, in order to improve their physicochemical properties and biocompatibility for in vitro studies.