The HSCT (haematopoietic stem cell transplant) is a particular treatment for many haematological and non-haematological diseases. Broadly, there are three different categories of transplantation, autologous, allogeneic and syngeneic, which can be applied to most disease scenarios. Haematopoietic stem cells can be derived from the bone marrow, peripheral blood and umbilical cord blood. HSCT treatment can be divided into separate phases that start with the harvest of the stem cells and passing through the conditioning, aplasia and engraftment until the recovery of the haematopoietic functions. HSCT is indicated in many diseases, and these indications depend on numerous factors such as the disease type, stage and response to previous treatment. Among non-malignant diseases, aplastic anaemia, sickle cell disease and, more recently, autoimmune diseases can also be effectively treated with HSCT. One third of the transplants in children are performed for rare indications such as severe combined immunodeficiencies. Allogeneic HSCT can also cure a number of non-malignant diseases in children, such as Wiskott-Aldrich syndrome and chronic granulomatous disease (CGD). This chapter will include transplant in primary immunodeficiency in children as well as inherited bone marrow failure and inborn errors of metabolism.