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The corneal epithelium is generally removed before photoablation in photorefractive keratectomy (PRK) because laser transepithelial PRK may result in surface irregularity caused by variability in epithelial thickness and differing ablation rates between epithelium and stroma. We compared the effects of mechanical deepithelialization with chemical epithelial removal by using 50% ethanol on the corneal structure.Fourteen rabbits underwent corneal deepithelialization by using a blade in the left eye and 24 h later in the right eye. Another 14 rabbits underwent corneal deepithelialization by using 50% ethanol solution. Half of the eyes treated with each technique underwent PRK after deepithelialization. Pachymetry was performed before and after each procedure on right eyes. Keratocyte and neutrophil densities were assessed by light microscopy.Among non-laser-treatment groups, eyes that underwent mechanical deepithelialization had decreased corneal thickness (p = 0.001), increased keratocyte densities (p = 0.03), and no significant difference in neutrophil densities (p = 0.91) compared with chemically treated eyes 24 h after surgery. Among laser-treatment groups, eyes that underwent mechanical epithelial removal had increased keratocyte densities (p = 0.001), decreased corneal thickness (p = 0.03), and increased neutrophil densities (p = 0.03) 24 h after surgery compared with chemically treated eyes.Deepithelialization with 50% ethanol causes more keratocyte loss with perhaps more corneal edema, but less stromal influx of neutrophils, than does a mechanical technique 24 h after PRK in a rabbit model. Corneal deepithelialization with dilute ethanol may be a viable option in PRK. However, further investigation into the safety of this technique is warranted before it can be widely applied clinically.