The detection of early-stage keratoconus is one of the most important safety issues in screening candidates for corneal refractive surgeries. We propose to use epithelial thickness maps to assist the diagnosis of keratoconus. The corneal epithelial thickness in normal and keratoconic eyes was mapped with optical coherence tomography (OCT). A Fourier-domain OCT system capable of acquiring 26,000 axial-scans per second was used. It has an axial resolution of 5μm in cornea. A pachymetry scan pattern (8 radials, 1024 axial-scans each, 6mm diameter, repeat 3 times) centered at the pupil center was used to image the cornea. The 3 repeated radial scans on each meridian were registered and averaged. Then the anterior corneal, posterior corneal and epithelial boundaries were segmented automatically with a computer algorithm by increased signal intensity at corresponding boundaries. The epithelial thickness map was generated by interpolating epithelial thickness profile calculated from each meridian. Normal and keratoconic eyes (24 eyes each) were scanned 3 times. The central epithelial thickness in normal eyes was thicker than those of keratoconic eyes (mean difference 2.1 μm, t-test p=0.05). The epithelium was thinner superiorly than inferiorly in normal eyes (mean difference -1.4±1.1μm, p<0.001) while thicker superiorly than inferiorly in keratoconic eyes (2.0±4.1 μm, p=0.02).