Fluorescent labeling based on silica nanoparticles facilitates unique applications in bioanalysis and bioseparation. Dye-doped silica nanoparticles have significant advantages over single-dye labeling in signal amplification, photostability and surface modification for various biological applications. We have studied the formation of tris(2,2'-bipyridyl)dichlororuthenium(II) (Ru(bpy)) dye-doped silica nanoparticles by ammonia-catalyzed hydrolysis of tetraethyl orthosilicate (TEOS) in water-in-oil microemulsion. The fluorescence spectra, particle size, and size distribution of Ru(bpy) dye-doped silica nanoparticles were examined as a function of reactant concentrations (TEOS and ammonium hydroxide), nature of surfactant molecules, and molar ratios of water to surfactant (R) and cosurfactant to surfactant (p). The particle size and fluorescence spectra were dependent upon the type of microemulsion system chosen. The particle size was found to decrease with an increase in concentration of ammonium hydroxide and increase in water to surfactant molar ratio (R) and cosurfactant to surfactant molar ratio (p). This optimization study of the preparation of dye-doped silica nanoparticles provides a fundamental knowledge of the synthesis and optical properties of Ru(bpy) dye-doped silica nanoparticles. With this information, these nanoparticles can be easily manipulated, with regard to particle size and size distribution, and bioconjugated as needed for bioanalysis and bioseparation applications.