Gene therapy holds promise in preventing the development of many diseases. One of the possible applications is the management of organ transplantation. Over the years, advances in vector development have allowed the clinical progression of this form of therapy to become more attainable. Viral vector technology has proved to be better than non-viral vectors at ferrying therapeutic genes to cells. However, many deficiencies in viral vectors hinder the full realisation of gene-based therapy in transplantation. Here, these deficiencies and their ramifications for the future of viral vector development are fully analysed. The authors propose that the slow progress of gene therapy in transplantation may be related to the deficiencies in viral vectors.