The term fluorescence is derived from the mineral fluorspar (calcium fluoride). Fluorescence belongs to the photoluminescence group of optical phenomena. It is a process where a molecular fluorescent dye (fluorochrome) absorbs a high-energy photon and more or less instantaneously re-emits a longer-wavelength photon. Upon absorption of the incoming photon, an electron of the fluorochrome is excited to a higher energy level. After a slight relaxation (vibrational and rotational energy loss) within the excited state, the electron drops back to its ground state and releases the excess energy via emission of a photon which has a slightly lower energy compared to the one which caused the excitation. This is why the emitted light has a different colour (longer wavelength); it is said to be red-shifted. This wavelength difference is also referred to as the Stokes shift. The energy difference between the absorbed and emitted photons ends up as molecular vibrations (heat).

Fluorescence microscopy is an invaluable tool especially for biomedical research and the field of biomedical applications is rapidly expanding. Fluorescence microscopy is widely used to identify cells and sub-microscopic cellular components with a high degree of specificity and exquisite sensitivity and has become an indispensable qualitative and quantitative detection technique. This is in part due to the development of a growing list of specific fluorochromes over a wide range of colours. Biological macromolecules can be labelled with a fluorescent chemical group attached by a chemical reaction. The fluorescent tag subsequently enables very sensitive detection of the molecule. Antibodies labelled in this way are common tools in fluorescence microscopy. In this case the sites on a microscopic specimen where the antibody has bound can be visualised by the fluorescence. One of the advantages over transmission light microscopy is that the presence of fluorescent molecules in structures below the diffraction limit can be visualised even if their spatial resolution cannot be provided.
Many biological molecules have an intrinsic fluorescence that can be utilised without the need to attach a synthetic chemical tag like green fluorescent protein (GFP) and related proteins. They are used as reporters for a large number of biological events including such things as sub-cellular localization or levels of gene expression.
Consequently fluorescence microscopy in bioscience has progressed from a purely structural characterization of fixed cells and immunofluorescence techniques towards newly developed methods that are suitable for life cell imaging. Dynamic processes such as cell growth, metabolic transport and signal transduction are monitored routinely nowadays. Examples are the study of rapidly changing ion concentrations (calcium etc.) and pH values in living cells or cell compartments. By the use of multiple staining, different probes or dyes will reveal the presence of different target molecules simultaneously within one sample. The observance and documentation of such dynamic phenomena creates substantial demands for the temporal resolution and data processing. Only with the advent of fast computers and highly sensitive, fast digital cameras with high spatial resolution, have these studies become possible.
In materials science fluorescence microscopy is used to investigate certain inorganic materials and in chip production it is especially useful to detect contaminants on semiconductor wafers.