Because it provides much higher magnification and better optical sectioning than a slit-lamp biomicroscope, confocal microscopy is ideally suited for clinical imaging of the cornea. One important clinical application of confocal microscopy has been the early detection and diagnosis of a number of infectious conditions, including infection with Acanthamoeba and microsporidium species, fungal keratitis, and contact lens-associated bacterial keratitis. Confocal microscopy has also been used for temporal evaluation of corneal wound healing following refractive surgery and penetrating keratoplasty. With the development of the new technique of quantitative confocal microscopy through-focusing, confocal microscopy can be used to measure epithelial, stromal, and corneal thickness accurately and reproducibly in human patients. Furthermore, conofocal microscopy through-focusing can be used to determine the initial photoablation depth, changes in epithelial, stromal, and corneal thickness, and subepithelial haze following photorefractive keratectomy.