Silica mesoporous nanoparticles have been recently selected for a wide range of applications from electronics to medicine due to their intrinsic properties. Among medical applications, drug delivery using SiO(2) nanoparticles by oral route is under study. Major benefits are expected including higher specificity and sensitivity together with side effect reduction. Since literature shows that very complex and unexpected interactions could occur between nanomaterials and biological systems, one critical issue is to control the nanoparticle cytotoxicity/genotoxicity for normal tissues and specially stomach and intestine when oral route is considered. The aim of the work is to study the cytotoxicity and genotoxicity of SiO(2) nanoparticles on HT29 human intestine cell line, using conventional and innovative methodologies, for measuring cell viability and proliferation, global metabolism, genotoxicity, and nanoparticles uptake. Core-dye doped SiO(2) nanoparticles of 25 and 100 nm were specifically synthesized to track nanoparticles incorporation by confocal and video microscopy. Besides conventional approaches (sulforhodamine B, flow cytometry, and γ-H2Ax foci), we have performed a real-time monitoring of cell proliferation using an impedance-based system which ensure no interference between measures and nanoparticles physicochemical characteristics. Overall, our results showed that SiO(2)-25nm and SiO(2)-100nm induced a rather limited cytotoxic and genotoxic effects on HT-29 cells after a 24 h exposure. However, regarding cell viability and genotoxicity, inverse dose-dependent relationships were observed for SiO(2)-100nm nanoparticles. In conclusion, it seems that the higher the dose of SiO(2)-100nm, the lower the cytotoxic/genotoxic effects, data that well illustrate the complexity in identifying and understanding the hazards of nanoparticles for human health.