Salt stress is a rising threat to crop productivity, among several notable consumed crops tomato is often under threat due to salt stress. In this study, the role of Si in restraining salinity stress responses in root proteome and genes involved in stress tolerance has been studied. Fifteen days old tomato (Lycopersicon esculentum L.) plants grown hydroponically with or without NaCl were fed with 2.5 mM Si in the form of potassium silicate [K2SiO3]. The response to a combined effect of NaCl and Si were studied 5 days after treatment. Proteomic analysis indicated that 40 proteins were differentially expressed under Si and/or salt stress treatments. Twenty-four of them were up-regulated by Si supplements (50 mM +NaCl/+Si) and down-regulated in salt-stressed roots (50 mM +NaCl/−Si), and these proteins were mostly associated with stress responses, plant hormones and transcriptional regulations. The rest of them belong to other secondary metabolites. Moreover, 17 differentially expressed proteins (25 mM +NaCl/+Si), up-regulated in the Si treatments, were mostly related to stress responses, plant hormones and cellular biosynthesis, and the rest of the proteins were related to transcriptional regulation, RNA binding and other secondary metabolisms. In addition, 17 protein spots were observed absent in salinity-stressed roots (25/or 50 mM +NaCl/−Si). Moreover, the important genes associated with salt stress responses (leDREB-1, leDREB-2 and leDREB-3), antioxidants (leAPX, leSOD and leCAT genes) and Si transport (leLsi-1, leLsi-2 and leLsi-3) were analyzed by the real-time polymerase chain reaction. The physiological data such as thiobarbituric acid reactive substances, superoxide dismutase as an oxidative stress marker and concentration of Si all correlated well with proteomic and gene expression data. The observed responses to Si supply in salt stressed plants indicate that the Si has a substantial role in alleviating the salinity stress responses by improving the root proteome and activating important genes responsible for stress tolerance. © 2015, Springer Science+Business Media Dordrecht.