Fundus autofluorescence (FAF) is a noninvasive, in vivo imaging technique that allows mapping of fluorophores in the retina. The technique can be used to evaluate a variety of retinal diseases that involve either abnormal fluorophore accumulation or the loss of fluorophores, such as in retinal pigment epithelium (RPE) atrophy. Conditions in which FAF can be informative include age related macular degeneration (AMD), Stargardt disease, and Best disease. By allowing clinicians to see details that may not be clinically visible, FAF can aid in the diagnosis, documentation, and assessment of disease. New techniques such as the ability to quantitate the FAF signal may allow deeper understanding of these conditions and improve our ability to predict their course.