Titanium dioxide nanoparticles are widely used in consumer products, paints and pharmaceutical preparations. They have been shown to induce cytotoxicity, genotoxicity and carcinogenicity—in vitro and in vivo. So far there is lack of standardized protocol for in silico analysis of nano-toxicological evaluations. In the present study, it was attempted to analyze the titanium dioxide nanoparticles-protein interaction through docking using AutoDock 4.0.5 software. Titanium dioxide nanoparticles with particle size of 1.09 nm were docked with different cellular proteins. Binding site area and volume has been determined by using CastP online server and docking has been performed at the active site as a pocket. The docked structures were analyzed for the most efficient binding with amino acids. It is the first study to report the interaction of titanium dioxide nanoparticles without any surface modification with proteins using docking analysis. The negative binding and docking energy inferred that the interaction of titanium dioxide nanoparticles with certain proteins is significant. Titanium dioxide nanoparticle shows significant interaction with intercellular adhesion molecule-1, P38 mitogen-activated protein kinases (P-38), placental growth factor and nuclear factor kappa-light-chain-enhancer of activated B cell proteins. Further, it has been observed that titanium dioxide nanoparticles show frequent interaction with proline, lysine as well as leusine. © 2015, The National Academy of Sciences, India.