Stem cell transplantation (SCT) is used to cure or greatly ameliorate a wide variety of genetic diseases, ranging from inherent defects of haemopoietic cell production or function to metabolic diseases mostly affecting solid organs. It ranks as one of the most remarkable therapeutic advances of the past 40 years. Despite rapid technological improvements, however, there are still many short term risks and potential long term toxicities. As a consequence, the rapid emergence of alternative therapies (including new drugs, enzyme and gene therapies), necessitate constant re-evaluation of the risk/benefit ratio for each disease and hence the appropriateness of SCT. This review describes the major aspects of the transplant process, indications for transplantation, outcome statistics, and areas where alternative therapies are becoming available.