Irreversible immunological rejection is the major cause of clinical corneal graft failure. Ex vivo gene therapy directed at the donor cornea has been shown to prolong orthotopic corneal allograft survival significantly in experimental animal models including the mouse, rat, rabbit, and sheep. Transgenes effective in prolonging corneal graft survival include immunomodulatory cytokines and cytokine receptors, an inhibitor of neovascularisation, a blocker of antigen-presenting cell-T cell co-stimulation, nerve growth factor, a dominant negative regulator of apoptosis, and the enzyme indoleamine 2,3-dioxygenase. Although many viral and non-viral vectors have been shown to transduce the corneal endothelium efficiently, allograft survival has so far been prolonged only following transduction of the donor cornea with adenoviral and lentiviral vectors. The degree of graft prolongation, although promising, is still insufficient for immediate translation to the clinic. Increasing the time that the therapeutic gene is expressed in the eye with an integrative, non-immunogenic viral vector is likely to be one way to achieve long-term graft survival. Simultaneous targeting of multiple pathways of graft rejection with more than one transgene is likely to be another. We suggest that the use of an adeno-associated viral or lentiviral vector combined with multiple transgenes may provide the key to future clinical trials.