Methods and compositions for the treatment of a corneal dystrophy in a subject in need thereof are provided. In one aspect, the method includes the step of obtaining a plurality of stem cells comprising a nucleic acid mutation in a corneal dystrophy target nucleic acid from the subject and manipulating the nucleic acid mutation in one or more stem cells of the plurality of stem cells to correct the nucleic acid mutation, thereby forming one or more manipulated stem cells. The manipulated stem cells are isolated and then transplanted into the subject. In some embodiments, the nucleic acid mutation is manipulated using CRISPR system.