Corneal endothelium is as crucial for maintenance of corneal function as difficult it is to be accessed with any treatment that doesn’t involve invasive surgical procedures. Hovewer it is possible to administer therapeutic agents by topical application, their effect on deeper corneal layers and further fate remains of our control. This study has been designed to employ nanoparticles in order to improve our chances in therapy of corneal dystrophies as well as to prevent endothelial cell loss after transplantation of the cornea. Variety of nanoparticles serves a potential solution to problem of targeting the corneal endothelium, when properly functionalized to assure precise targeting. Widely proven as efficient carrier for nucleic acids may enable any gene therapy or gene silencing to be conducted with minimized risk of uncontrolled transfection. When to concern both growing need for corneal transplantations and shortage of tissue, efficient therapy to protect graft from failure or even to protect patient’s own cornea becomes essential.