Although endothelial cells are not immunological cells in sensu stricto, they play an important role in controlling inflammation/immune responses. The endothelium is involved in a wide range of pathologies, the most common being vascular diseases and cancer, and they also are central to transplant rejection. Genetic modification of endothelium allows different strategies for inducing tolerance, modulating inflammation, stimulating the immune response or inhibiting the formation of new blood vessels. In this context, the lack of effective and specific pharmacological interventions renders endothelial cells extremely attractive for gene therapy applications. Despite efforts made to genetically modify endothelial cells, the results obtained have suffered from the differences of the endothelium at the different anatomical sites. Several studies are currently being developed to specifically target endothelium using viral and non viral gene delivery approaches. We highlight here some strategies used for genetically manipulating endothelial cells with the aim of inducing tolerance to allograft, or enhancing immunity and/or inhibiting uncontrolled endothelial cell proliferation in tumours.