PURPOSE: To illustrate the value of confocal microscopy and chromatrope stain in the diagnosis of microsporidial keratitis. METHODS: In vivo confocal microscopy was performed on a man with the human immunodeficiency virus who had severe bilateral epithelial keratitis refractory to topical antibacterial medications. The results were compared to conjunctival scrapings stained with the chromatrope-based Weber stain. RESULTS: Confocal microscopy demonstrated many small, intraepithelial opacities of the corneal epithelium, which were suggestive of Microsporidia. Results of the chromatrope stain of conjunctival scrapings confirmed the diagnosis of microsporidial keratitis. CONCLUSIONS: Rapid diagnosis allowed prompt initiation of topical fumagillin, which permitted rapid, long-term control of the symptoms of microsporidial keratitis.