BACKGROUND In clinical practice, the differentiation of glaucomatous from non-glaucomatous cupping can be difficult, even for experienced observers. The purpose of this study was to evaluate the role of optical coherence tomography (OCT) in differentiating glaucomatous from non-glaucomatous optic nerve cupping in a cross-sectional pilot study. METHODS Eleven consecutive patients presenting to the Duke Eye Center from September 2007 to July 2008 with non-glaucomatous optic nerve cupping and 12 patients with glaucomatous optic nerve cupping were identified. All patients underwent Stratus® OCT imaging: fast macular map, fast retinal nerve fiber layer (RNFL) 3.4 thickness, and fast optic disc protocols. Automated visual field perimetry was performed on the date of OCT scan in non-glaucomatous cupping patients, and from 0-9 months of scan date in glaucoma patients. Eyes were matched by optic nerve cup-to-disc area ratio; average and mean deviation were calculated for each variable. RESULTS For a similar average RNFL, patients with non-glaucomatous optic nerve cupping had lower nasal and temporal RNFL thickness, as well as lower macular thickness and volume compared to patients with glaucomatous optic nerve cupping. CONCLUSIONS OCT appears to be a useful technology in differentiating glaucomatous from non-glaucomatous optic nerve cupping. The pattern of RNFL loss appears more diffuse in non-glaucomatous optic nerve cupping compared to glaucomatous optic nerve cupping. Future studies with larger sample size and specific neuro-ophthalmic causes of optic nerve cupping may further elucidate the role of OCT in this clinical setting.