Epoxy-organosilica particles made from 2-(3,4-epoxycyclohexyl)ethyltrimethoxysilane (EpoMS) as a single silica source were synthesized by means of a one-pot method. We evaluated three sets of synthesis conditions, including traditional Stober conditions and two variations. Although the traditional conditions did not afford EpoMS particles, the variations did. The size distributions of the particles were evaluated by means of transmission electron microscopy. The mean diameters and size distributions of the particles depended on the EpoMS concentration, and the best coefficient of variation for the size distribution was 5.9%. The surface of the particles had unique properties, such as a positive zeta potential. The particles bound strongly to proteins as well as to DNA. The particles made from EpoMS, allowing particles internally functionalized with fluorescent dye to be prepared by means of a one-pot synthesis. EpoMS particles doped and tuned with fluorescent dye showed strong fluorescence signals and distinct peaks on flow cytometry, and the fluorescent particles could be used to label cells. The labeled cells showed clear fluorescence under a fluorescence microscope, and electron microscopy showed many particles in the cytoplasm. This is the first report describing the synthesis of epoxy-organosilica particles with a positive zeta potential and describing differences in the characteristics of particle formations due to changes in synthesis conditions. We also discuss the advantages of EpoMS particles, as well as the potential biological applications of these particles.