Purpose: To analyze the relationship between drusen morphology revealed by spectral-domain optical coherence tomography (SD-OCT) and corresponding fundus autofluorescence (FAF) features of the same drusen using the Heidelberg Retina Angiograph 2 (HRA2), in patients with dry age-related macular degeneration (AMD). Methods: Dry AMD patients were imaged with SD-OCT and HRA2 on the same day. SD-OCT B scans were then precisely overlaid onto the HRA2 images, and the SD-OCT morphological characteristics of the drusen were correlated with the corresponding FAF appearance. The analyzed morphological features of the drusen included: size, status of the inner segment/outer segment (IS-OS) junctional layer above the drusen, shape of the drusen, internal reflectivity, homogeneity and presence of overlaying hyperreflective foci. The FAF characteristics of each druse were rated as hyperautofluorescent, hypoautofluorescent or normally autofluorescent. Spearman’s correlation coefficient was used to analyze the correlation between the 2 primary outcomes: SD-OCT morphology of the drusen and their autofluorescent appearance. Results: 431 drusen in 32 eyes of 16 dry AMD patients were evaluated. Of the 7 morphological characteristics assessed by SD-OCT, only drusen size and the status of the IS-OS layer above the drusen were strongly correlated with the autofluorescent appearance (r = 0.78, p < 0.001, and r = 0.58, p < 0.001, respectively). The strength of correlation with other features appeared less robust: homogeneity (r = 0.38; p = 0.001), shape (r = 0.29; p = 0.004), reflectivity (r = 0.28; p = 0.004) and presence of overlaying foci (r = 0.25; p = 0.12). Conclusions: Autofluorescent changes most strongly correlate with drusen size and disruption of the IS-OS layer and may be useful as an additional functional-morphological feature by which drusen and their impact upon overlying photoreceptors may be judged.