A number of dye-doped silica nanoparticles (DDSNs) have been developed by encapsulating various fluorophores into silica nanomatrixes. These DDSNs have shown great potential as highly sensitive fluorescent labeling agents for biosensing and bioimaging. The silica nanomatrix affects the radiative properties and reactivity of doped fluorophores and endows the DDSN surface properties of silica. Compared with molecular fluorophores, the DDSNs exhibit advantageous properties such as high fluorescence intensity, good photostability, and biological compatibility. In this chapter, methods for silica nanoparticle synthesis and approaches for doping dye molecules within the silica nanomatrixes are overviewed. Various advantageous properties of DDSNs are discussed including reaction kinetics, solubility, photostability, quantum yield, lifetime, and toxicity.