Prevention of acute rejection has been well controlled with immunosuppressive drugs. However, the long-term control of rejection is less satisfactory and the side effects of chronic usage of these drugs are far from acceptable. Thus, more imaginative options for therapy need to be explored. Gene therapy has potential promise in preserving allografts, preventing rejection and inducing tolerance. Despite this initial promise in many animal models, the translation of gene therapy to the clinical arena has been slow. This may be related in part to the deficiencies in vector development. Existing viral vectors are efficient at transducing allografts, but they induce inflammatory and pathogenic effects. Although the alternative non-viral systems are relatively innocuous, they are less efficient at gene delivery. This review systematically analyses the limitations of non-viral vector technology and the strategies that have been developed to overcome these limitations. Future development of non-viral vectors may have potential application in clinical transplantation.