Fundus autofluorescence (FAF) imaging allows for non-invasive mapping of changes at the level of the retinal pigment epithelium/photoreceptor complex and of alterations of macular pigment distribution. This imaging method is based on the visualisation of intrinsic fluorophores and may be easily and rapidly used in routine patient care. Main applications include degenerative disorders of the outer retina such as age-related macular degeneration, hereditary and acquired retinal diseases. FAF imaging is particularly helpful for differential diagnosis, detection and extent of involved retinal areas, structural-functional correlations and monitoring of changes over time. Recent developments include - in addition to the original application of short wavelength light for excitation ("blue" FAF imaging) - the use of other wavelength ranges ("green" or "near-infrared" FAF imaging), widefield imaging for visualisation of peripheral retinal areas and quantitative FAF imaging.