The first hematopoietic stem cell transplantation (HSCT), the replacement of the hematopoietic system, by hematopoietic stem cells from the patient (autologous HSCT) or from another person (allogeneic HSCT), was performed almost 45 years ago. Today autologous HSCT is used to bridge hematopoietic failure after high dose chemotherapy for the treatment of selected hematopoietic and non-hematopoietic tumours. Allogeneic HSCT is used to treat congenital or acquired marrow failure, and, more commonly, to exploit the graft versus tumour effect of allogeneic cells against high risk hematologic malignancies. In 2010, 30,000 patients were treated with HSCT (12,000 allogeneic and 18,000 autologous HSCT) in Europe. Substantial progress has been made in the field of allogeneic HSCT in the last decade. First the article describes advances in patient and donor selection, the current concepts of choosing the optimal stem cell source and the most appropriate preparative regimen. Furthermore, recent advances in supportive care are described. We describe how these innovations have allowed indications for allogeneic HSCT to be expanded. Finally, prospects for future developments will be outlined.