Haematopoietic stem cell transplantation (HSCT) is an established curative treatment for many malignant and non-malignant diseases. Over the last two decades, novel approaches have resulted in significant reductions in the morbidity and mortality associated with HSCT. These include the utilisation of reduced intensity regimens, more effective graft versus host disease prophylaxis, exploration of new sources of progenitor haematopoietic stem cells and better prophylaxis and treatment of infections. Despite current advances, new strategies are needed to further reduce the complications associated with HSCT. This article reviews the current indications for HSCT and the recent progress in the field of both allogeneic- and autologous HSCT.