Haematopoietic stem cell transplantation is used clinically to treat many haematological conditions. Isolation of a patient’s own stem cells is a feasible approach for gene therapy and autologous transplantation, which removes the requirement for an immunologically matched donor and the restriction this causes. Manipulating the genome of blood progenitor cells is possible and represents a promising approach to correct genetic and acquired disorders using the patient’s own material. However, the efficiency and safety of gene correction in these stem cells is not yet at the level required for translation into large-scale clinical application. Current approaches, challenges and possible solutions will be discussed.