The present invention provides a fluorescent silica-based nanoparticle that allows for precise detection, characterization, monitoring and treatment of a disease such as cancer. The nanoparticle has a fluorescent compound positioned within the nanoparticle, and has greater brightness and fluorescent quantum yield than the free fluorescent compound To facilitate efficient urinary excretion of the nanoparticle, it may be coated with an organic polymer, such as polyethylene glycol (PEG). The small size of the nanoparticle, the silica base and the organic polymer coating minimizes the toxicity of the nanoparticle when administered in vivo. The nanoparticle may further be conjugated to a ligand capable of binding to a cellular component associated with the specific cell type, such as a tumor marker. A therapeutic agent may be attached to the nanoparticle. Radionuclides/radiometals or paramagnetic ions may be conjugated to the nanoparticle to permit the nanoparticle to be detectable by various imaging techniques.