We treated a patient with chronic keratitis caused by Mycobacterium gordonae, a slow-growing, atypical mycobacterium not previously reported as a cause of corneal infection. The patient was a 34-year-old man who was hit in the eye with some vegetable matter while gardening. Initially, the patient was treated for a presumptive diagnosis of herpes simplex keratitis. Because of progression of the keratitis, a lamellar corneal biopsy was performed 3 1/2 years later and the definitive diagnosis was made. Subsequently, a penetrating keratoplasty was performed and the patient's condition then remained stable. The diagnosis of atypical mycobacterium should be considered in a patient with an indolent corneal ulcer. Lamellar corneal biopsy may disclose the pathogen when the infection is deep, chronic, or partially treated.