Autologous hematopoietic cells have been used as targets of gene transfer, with applications in inherited disorders, cell therapy, and acquired immunodeficiency. The types of cells include hematopoietic progenitor cells, lymphocytes, and mesenchymal stem cells. The inherited disorders thus far approached in clinical trials include severe combined immunodeficiency, common variable γ-chain immunodeficiency, chronic granulomatous disease, and Gaucher disease. Preclinical studies are vigorously under way in thalassemia, sickle cell anemia, Wiskott-Aldrich syndrome and Fanconi anemia. Clinical trials of immunological therapy with gene-modified lymphocytes are under study in the treatment of malignancies. Clinical trials using anti-viral strategies for HIV infection in combination with autologous transplantation have begun, with additional approaches being developed. Gene therapy vectors are being developed to eliminate tumor cells contaminating autologous stem cell products. However, the risk of insertional mutagenesis and the potential for development of leukemia was highlighted by the first gene therapy trials in inherited immunodeficiency syndromes that achieved a therapeutic effect. Despite the slow progress of the field to date, there is extraordinary promise for gene therapy in the future.