In transplantation, gene therapy strategies to prolong graft survival involve gene transfer and expression of immunomodulatory or graft-protecting molecules. The local production of immunosuppressive molecules has the potential to reduce their systemic side effects, and to increase their bioavailability and hence their therapeutic efficiency. Ex vivo gene transfer enables manipulation prior to engraftment. Vectors have now been developed that can optimally transfer the relevant genes to various cells, tissues and organs. The elimination of genetically modified cells can even be time-controlled by prodrug administration in suicide gene therapy systems. Gene transfer to stem cells may eventually lead to accelerated tissue repair and regeneration. In addition, xenotransplantation and organ cloning techniques have the potential to resolve the current shortage of donor organs.