BACKGROUND: To apply automated spectral domain optical coherence tomography (SD-OCT) segmentation to eyes with resolving papilledema. METHODS: Ninety-four patients with idiopathic intracranial hypertension seen at the Duke Eye Center neuro-ophthalmology clinic between November 2010 and October 2011 were reviewed. Excluded were eyes with papilledema with Frisén grade >2, other optic neuropathies or retinopathies, and those that did not have SD-OCT imaging. The remaining 43 patients were split into 2 groups: non-atrophic papilledema and atrophic papilledema. Automated SD-OCT segmentation was performed on patients with non-atrophic papilledema and age-matched controls for each of the 9 regions of the Early Treatment Diabetic Retinopathy Study map. Bonferroni correction was used for multiple comparisons. All SD-OCT scans were reviewed for retinal structural abnormalities. RESULTS: Total macular thickness was significantly thinner within the fovea and inner macular ring in non-atrophic papilledema vs control eyes (266 vs 276 μm, P = 0.04; 333 vs 344 μm P < 0.01, n = 26 non-atrophic papilledema, 30 controls). SD-OCT demonstrated thinning within the fovea, inner macular ring, and outer macular ring of the outer plexiform layer plus nuclear layer in non-atrophic papilledema vs control (124 vs 131 μm, P < 0.01; 112 vs 118 μm, P = 0.03; 95 vs 100 μm, P = 0.03). Retinal structural changes were seen in 21/33 eyes with atrophic papilledema vs none of the eyes with non-atrophic papilledema or controls. CONCLUSIONS: SD-OCT shows qualitative and quantitative changes in the macula of eyes with resolved papilledema.