Stem cell transplantation plays a pivotal role in the management of many haematological malignancies and is an increasingly important therapeutic option in non-malignant haematological and auto-immune diseases. Advances in supportive care and the use of mobilised peripheral blood stem cells have substantially reduced the morbidity and mortality of autologous transplant, such that it is now often delivered as an out-patient, but disease relapse remains the major cause of transplant failure. Increased donor availability, the advent of reduced intensity conditioning regimens and improved strategies to prevent and treat graft-versus-host disease have steadily increased the number of patients who can benefit from the curative potential of allogeneic transplantation. However despite the presence of an often potent graft-versus-leukaemia effect disease relapse remains the major cause of treatment failure post-allograft. A number of innovative strategies have the potential to reduce the risk of post-transplant relapse and include optimising the conditioning regimen and the use of post-transplant maintenance using pharmacological agents or cellular therapies. The increased effectiveness of non-transplant treatment options coupled with the importance of reducing the risk of relapse post-transplant only serves to underline the importance of prospective randomised transplant trials if patient outcomes are to improve and investment in national and international transplant trial networks is an important priority for the future.