A monochromatic beam of light (typically a laser beam) is directed onto a hydrodynamically focused stream of fluid. Multiple detectors are aimed at the point where the stream passes through the light beam; one in line with the light beam, and several perpendicular to it. Each suspended particle passing through the beam scatters the light in some way; in addition, fluorescent chemicals in the particle may be excited into emitting light at a lower frequency than that of the incident light. This combination of scattered and fluorescent light is picked up by the detectors. By analysing fluctuations in brightness at each detector—one for each fluorescent emission peak—it is possible to infer various facts about the physical and chemical structure of each individual particle.

Modern flow cytometers can analyse several thousand particles per second in real time. They can actively separate out and isolate particles having specified properties.

(This text is based in part on the Wikipedia entry on flow cytometry.)