A method of corneal transplantation with a cross-linked cornea is disclosed herein. In one or more embodiments, the method includes the steps of: (i) cross-linking a portion of a donor cornea so as to kill donor keratocytes in the donor cornea and make the cross-linked donor cornea less antigenic to an eye of a recipient patient (ii) removing a scarred and/or diseased cornea or corneal portion from the eye of the recipient patient and (iii) implanting the cross-linked donor cornea into the eye of the recipient patient in a location previously occupied by the scarred and/or diseased cornea or corneal portion, wherein the cross-linking of the donor cornea eliminates an immune response of the recipient patient to the transplanted donor cornea. Both penetrating keratoplasty transplant procedures and lamellar keratoplasty transplant procedures using a cross-linked donor cornea are disclosed herein.