FITC is a fluorochrome often conjugated or linked to an antibody in order to make a specific, fluorescent marker. When exposed to electromagnetic energy at a specific wavelength, fluorochromes are chemicals that will absorb the energy and emit a photon at a specific wavelength. FITC absorbs energy at 495 nm and emits a photon at 521 nm. Each fluorochrome has a different absorption and emission range, allowing for systematic detection of many fluorchrome-linked antibodies in one piece of tissue or sample. This is similar to labeling different parts of a cell with different colors and then using specialized glasses to look at just one color at a time.

Antibodies can be linked, or conjugated, to the FITC molecule to produce a FITC antibody. This FITC antibody can be used to directly or indirectly label a protein. When a FITC antibody directly labels a protein, it acts as the primary antibody, or an antibody in direct contact with the antigen. Indirect use of a FITC antibody occurs when it is used as a secondary antibody, binding specifically to a primary antibody. When a FITC conjugated antibody is used directly, the labeling procedure takes less time, but the labeling is not as strong. Indirect labeling takes an extra step, but the signal or label is amplified because several FITC-tagged secondary antibodies can attach to a single primary antibody.