Hematopoietic stem and progenitor cells (HSC) have been widely used in allogeneic transplant procedures, therefore their intrinsic characteristics, the biology of their niche in the bone marrow, and the mobilization and homing processes have been extensively investigated. With the development of gene therapy strategies, new therapeutic options based on autologous HSC have become available which may reduce the morbidity and mortality associated to allogeneic transplantation, but require an ex vivo manipulation of the cells to be corrected before re-infusion. For the success of these approaches it is necessary to optimize culture conditions in order to achieve efficient cell transduction while preserving the biological properties of the stem cells. We review here the factors critical for achieving efficient HSC transduction and maintenance of HSC stemness and homing capacity upon ex vivo culture. When HSC gene therapy is used in genetic disorders, permanent integration of therapeutic genes into the chromosomes of affected cells is needed. Indeed, by use of integrating vectors, such as retroviruses, gene therapy has met significant success in immunodeficiency syndromes characterized by a selective advantage of the transduced cells. However, retroviral integration can take place in stem cells at a variety of chromosomal sites, and examples have been reported of integration of therapeutic vectors causing cancer in patients. The clinical benefit arising from the long-term correction of the genetic defect, due to vector integration into the HSC genome, and the adverse consequences of these events are also here discussed, together with the new and challenging perspectives of HSC gene therapy.