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Background Post-translational protein modification by lipid peroxidationproducts orglycation is a feature of aging as well as pathologic processes in postmitotic cells at the ocular fundus exposed to an oxidative environment. The accumulationofmodifiedproteinssuchasthose found inlipofuscinand advanced glycation end products (AGEs) contribute greatly to the fundus auto-fluorescence. The distinct fluorescence spectra of lipofuscin and AGE enable their differentiation in multispectral fundus fluorescence imaging. Method A dual-centre consecutive case series of 78 pseudophacic patients is reported. Digital colour fundus photographs as well as auto-fluorescence images were taken from 33 patients with age related macular degeneration (AMD), 13 patients with diabetic retinopathy (RD), or from 32 cases without pathologic findings (controls). Fluorescence was excited at 475–515 nm or 476–604 nm and recorded in the emission bands 530–675 nm or 675–715 nm, respectively. Fluorescence images excited at 475–515 nm were taken by a colour CCD-camera (colour-fluorescence imaging) enabling the separaterecording of green and red fluorescence. The ratio of green versus red fluorescence was calculated within a representative region of each image. Results The 530–675 nm auto-fluorescence in AMD patients was dominated by the red emission (green vs. red ratio, g/r=0.861). In comparison, the fluorescence of the diabetics was green-shifted (g/r=0.946; controls: g/r= 0.869). Atrophic areas (geographic atrophy, laser scars) showed massive hypo-fluorescence in both emission bands. Hyper-fluorescent drusen and exudates, unobtrusive in the colour fundus images as well as in the fluorescence images with emission >667 nm, showed an impressive green-shift in the colour-fluorescence image. Conclusions Lipofuscin is the dominant fluorophore at long wavelengths (>675 nm or red channel of the colour fluorescence image). In the green spectral region, we found an additional emission of collagen and elastin (optic disc, sclera) as well as deposits in drusen and exudates. The green shift of the auto-fluorescence in RD may be a hint of increased AGE concentrations.