This review focuses on our basic study results and clinical experience of fluorescence endoscopy for the gastrointestinal (GI) tract. Collagen, which fluoresces in the green wavelength range, is one of the major sources of tissue autofluorescence (AF) and AF imaging systems are now available. With their use, however, it is important to take into account tissue changes other than, or in addition to, changes in gross tissue morphology. These may include alterations in the local blood volume, tissue metabolic activity, and relative fluorophore concentrations. New AF imaging systems are very easy to use, because white light endoscopy can be changed to AF at the push of a button, and hold great promise for diagnosis of early carcinomas and premalignant lesions in the GI tract. In particular, AF endoscopy has potential for identification of small or flat tumors, tumor margins and premalignant lesions in Barrett's esophagus, as well as for assessing tumor grade and response to therapy. However, large-scale studies are needed to clarify the clinical impact of this new diagnostic approach.