The comparative research of silica, the magnetite and magnetite-silica nanoparticles modified with fluorescent dyes using gas-phase and liquid-phase methods was conducted. At the content of fluorescent dye comparable in size a particular spectrophotometric method, nanoparticles with fluorescein have up to 1000 times larger overall luminous efficiency. It is revealed that magnetic nanoparticles are characterized by a smaller light efficiency in comparison with silica particles, at the same time particles of a magnetite are most effective at modification with fluorescein, and magnetite-silica particles - at modification with indocyanine green.