Beta-thalassaemia major and sickle-cell disease (SCD) reduce lifespan and quality of life for >300000 children and young adults worldwide. The only cure for both disorders is allogeneic stem cell transplantation (SCT). The decision-making processes in recommending SCT for patients with thalassaemia and SCD are different. For thalassaemia, where transfusion-related iron overload is universal, SCT should be offered to all patients <17 years because long-term survival and thalassaemia-free survival are about 80 and 70% respectively. For thalassaemics unable to comply with medical treatment, SCT offers a significant survival advantage; however, for patients with optimal medical care, short-term survival after SCT is inferior to medical treatment, and SCT instead offers a life free from transfusions and iron chelation. The clinical heterogeneity of SCD means that SCT is recommended only for selected patients with severe disease, particularly sickle-related neurological problems, for whom long-term survival and SCD-free survival after SCT approach 92 and 86% respectively. We here review the evidence available to help physicians evaluate the role of SCT for individual patients with thalassaemia major or SCD.