Fundus autofluorescence is a noninvasive imaging technology that provides information on the distribution of lipofuscin within the retinal pigment epithelial cell monolayer. Progressive accumulation of lipofuscin within retinal pigment epithelial cells is involved in the pathogenesis of geographic atrophy in age-related macular degeneration. This review contains an introduction to fundus autofluorescence, review of currently available imaging methods, and discussion of the role of autofluorescence imaging in geographic atrophy progression. The recent classification of geographic atrophy phenotypes by the Fundus Autofluorescence in Age-related Macular Degeneration Study (FAM) and the association of phenotype and atrophy progression are also summarized.