Primary immunodeficiencies constitute a group of highly complex congenital disorders commonly characterized by an extremely poor prognosis. Allogeneic hematopoietic stem cell transplantation has the potential to establish a permanently functioning immune system and represents a curative approach in many of these disorders. In this review several aspects of stem cell transplantation are presented, with an emphasis on the mechanism of immune reconstitution in severe combined immunodeficiency diseases. In this disorder transplant modalities vary, and also include transplantation without cytoreductive conditioning. Clinical results are summarized based on recent analysis performed in large patient cohorts, which have shown steady improvements and have led to a marked change in the prognosis of patients with primary immunodeficiencies.