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Vascular endothelial cells are an exposed target tissue for immune-mediated injury during graft-versus-host disease (GVHD). However, widespread endothelial death resulting in multi-organ failure similar to that in hyperacute solid-organ transplant rejection is not observed during GVHD. The rather mild endothelial injury seen in histological samples from affected skin biopsies contrasts with severe epithelial injury observed sometimes simultaneously. The elucidation of the mechanisms that influence endothelial susceptibility to immune-mediated injury would explain this paradox and may help to separate GVHD from the beneficial graft-versus-leukaemia effect. Transplant-associated microangiopathy, veno-occlusive disease and accelerated arteriosclerosis are vascular injury syndromes that occur after allogeneic stem-cell transplantation. Biomarkers are needed to identify individuals at risk of developing these complications. Treatments that have been found to be particularly effective for these specific endothelial injury syndromes need to be tested in larger clinical trials.