Corneal dystrophies are a rare group of hereditary disorders, that are bilateral, non-inflammatory, and progressive. Clinically, they can be classified based on the anatomic layer of the cornea affected. Refractive surgery and phototherapeutic keratectomy (PTK) can be performed with caution in patients with certain corneal dystrophies, but should be avoided in others. For epithelial basement membrane dystrophy, photorefractive keratectomy (PRK) is the procedure of choice for treatment of refractive error, and PTK may be performed for the treatment of recurrent erosions or irregular astigmatism. PRK and laser-assisted in situ keratomileusis (LASIK) have been associated with exacerbation of combined granular-lattice corneal dystrophy. LASIK and PRK appear to be safe in mild forms of posterior polymorphous corneal dystrophy, whereas LASIK should be avoided in Fuchs dystrophy. The safety of refractive surgery and PTK in the remainder of epithelial, Bowman layer, and stromal dystrophies has yet to be established.