Using a one-pot synthesis, thiol-organosilica nanoparticles (NPs) made from (3-mercaptopropyl)trimethoxysilane, (3-mercaptopropyl)triethoxysilane, and (3-mercaptopropyl)methyldimethoxysilane have been successfully prepared. We compared the synthesis processes of thiol-organosilica NPs made of these three kinds of organosilicates, as well as particles made from tetraethoxysilicate (TEOS), at concentrations varying between 6.25 and 200 mM. We examined three types of synthetic conditions: the Stöber method, in which particles are prepared in 65% ethanol, and two entirely aqueous solvent syntheses, containing either 2% or 27% ammonium hydroxide. The synthetic mixtures were examined using transmission electron microscopy (TEM) to evaluate the as-prepared NPs. The formation trends and rates for these organosilica NPs vary with differing organosilicate precursors, concentrations, and synthetic conditions. The Stöber method is not suitable for formation of thiol-organosilica NPs as compared with the case of TEOS, but the conditions without ethanol and with 27% ammonium hydroxide are suitable for the formation of thiol-organosilica NPs. The size distributions of the formed NPs were evaluated using TEM and dynamic light scattering. The mean diameters of NPs increase with increasing concentrations of silicate, but the size distributions of NPs prepared under various conditions also differ between silicate sources. Thiol-organosilica NPs internally functionalized with fluorescent dye were also prepared using a one-pot synthesis and were characterized using fluorescence microscopy. The thiol-organosilica NPs retain fluorescent dye maleimide very well. In addition, rhodamine B-doped thiol-organosilica NPs show higher fluorescence than thiol-organosilica NPs prepared with rhodamine red maleimide. The surface of thiol-organosilica NPs contains exposed thiol residues, allowing the covalent attachment of fluorescent dye maleimide and protein maleimide. This is the first report describing the synthesis of thiol-organosilica NPs made of three kinds of thiol-organosilicates, differences in nanoparticle formation due to the kinds and concentrations of thiol-organosilicate and due to synthetic conditions, and the advantages of thiol-organosilica NPs due to the existence of both interior and exterior thiol residues.