Purpose. To investigate morphologic alterations in geographic atrophy caused by age-related macular degeneration (AMD) in the presence of foveal sparing using high-resolution in vivo imaging. methods. Simultaneous spectral domain optical coherence tomography (SD-OCT, 870 nm, 40,000 A-scans/s) and confocal scanning laser ophthalmoscopy (cSLO; fundus autofluorescence; excitation, 488 nm; emission, 500–700 nm) were performed in 18 eyes with geographic atrophy and foveal sparing using a combined instrument. Anatomic layers were evaluated, and retinal thickness in the fovea and the peripheral macula were measured and compared with those in controls of similar age. results. Fundus autofluorescence imaging showed an inhomogeneously reduced signal at the residual foveal island. SD-OCT scans disclosed mitigation of the foveal pit in the absence of extracellular fluid accumulation and an increased mean central retinal thickness of 248 ± 28 μm compared with 225 ± 12 μm in control eyes (P = 0.005). No difference in retinal thickness in the peripheral macula was observed (245 ± 16 vs. 253 ± 11 μm; P = 0.6). Subanalysis revealed marked appearance of swelling and widening of visible structures at the central outer nuclear layer (153 ± 22 μm vs. 127 ± 12 μm; P = 0.003). Below the external limiting membrane, a broad band of irregular high reflectivity was detected instead of the normal three separate reflective bands. conclusions. Thickening at the foveal site may reflect a pre-apoptotic stage of neuronal cellular elements indicating imminent atrophy. Limited structure-function correlation found in our study suggests that future therapeutic intervention may be beneficial in only a subset of AMD patients with foveal sparing.