Purpose: To determine histologic correlates for stages of drusen-associated atrophy observed with fundus autofluorescence (FAF) and color fundus photography (CFP), of eyes with advanced age-related macular degeneration (AMD). Design: Case study and clinicopathologic correlation. Participant: A white woman with AMD findings of inactive subretinal fibrosis (right eye) and untreated nonexudative type 1 macular neovascularization (left eye) was followed for 9 years before death at 90 years of age. Methods: Eyes preserved 6.25 hours after death were postfixed in osmium tannic acid paraphenylenediamine and were prepared for submicrometer epoxy resin sections (115 and 90 from the right and left eye, respectively), with 19 aligned to clinical B-scans. Drusen visible by CFP at the last visit were assigned to 4 stages of FAF: stage 1, isoautofluorescence; stage 2, mildly uniform hyperautofluorescence; stage 3, a ring of hyperautofluorescence around a center of the hypoautofluorescence; and stage 4, uniform hypoautofluorescence. Main Outcome Measures: Light microscopic morphologic features at known FAF stages, including druse size, druse contents, and changes in overlying retinal pigment epithelium (RPE), photoreceptors, and external limiting membrane (ELM). Results: Histologic examination of 166 drusen demonstrated that stage 1 isoautofluorescent drusen were visible on CFP. Hyperautofluorescence in stage 2 corresponded to short photoreceptors and complete coverage by RPE. Hypoautofluorescence in stages 3 and 4 corresponded to different extents of RPE atrophy (RPE gap and no RPE, respectively). Of stage 4 drusen, 67% showed no outer nuclear layer (ONL) and an undetectable ELM. Stage 4 included a high proportion of refractile drusen (82%) with many calcific nodules, visible on CFP. Conclusions: We present the first direct clinicopathologic correlation for FAF imaging of drusen-associated atrophy. Our data support 4 FAF stages of drusen-associated atrophy. Stage 2 is the earliest detected stage in which loss of screening by photoreceptor photopigment contributes to uniform hyperautofluorescence. Stages 3 and 4 comport with incomplete RPE and outer retinal atrophy as defined by the Classification of Atrophy Meetings group. Loss of RPE, ONL, and ELM in stage 4 indicates that atrophy can begin over individual drusen. Findings will help the identification of new therapeutic approaches and clinical study end points.