Fluorescent silica nanoparticles (NPs) have potential in biomedical applications as diagnostics and traceable drug delivery agents. In this study, we have synthesized fluorescent dye grafted silica NPs in two step process. First, a stable method to synthesize various sizes of silica NPs ranging from 20 to 52, 95, 210 and 410 nm have been successfully demonstrated. Secondly, as-synthesized silica NPs are readily grafted with some fluorescent dyes like IR-820 and fluorescein isothiocyanate (FITC) dyes by simple impregnation method. IR-820 and FITC dyes are ‘activated’ by (3-mercaptopropyl)trimethoxysilane (MPTMS) and (3-aminopropyl)triethoxysilane (APTS) respectively prior to the grafting on silica NPs. UV–vis spectroscopy is used to test the stability of dye grafted silica NPs. The fluorescent dye grafted silica NPs are quite stable in aqueous solution. Also, a new type of dual dye-doped hybrid silica nanoparticles has been developed. The combination of microscopic and spectroscopic techniques shows that the synthesis parameters have significant effects on the particle shape and size and is tuneable from a few nanometers to a few hundred nanometers. The ability to create size controlled nanoparticles with associated (optical) functionality may have significant importance in bio-medical imaging.