The advent of Highly Active Antiretroviral Therapy (HAART) has radically changed incidence characteristics and prognosis of HIV-positive patients affected by lymphomas. At this time there is consensus in the literature that, in first line, HIV-positive patients should always be treated with curative intent preferentially following the same approach used in the HIV-negative counterpart. On the contrary, an approach of salvage therapy in HIV-positive lymphomas is still a matter of debate given that for a wide range of relapsed or resistant HIV-negative Hodgkin's disease (HD) and non-Hodgkin lymphoma (NHL) patients, autologous peripheral or allogeneic stem cell transplantation are among the established options. In the pre-HAART era, therapeutic options derived from pioneering experiences gave only anecdotal success, either when transplantation was used to cure lymphomas or to improve HIV infection itself. Concerns relating to the entity, quality, and kinetics of early and late immune reconstitutions and the possible worsening of underlying viroimmunological conditions were additional obstacles. Currently, around 100 relapsed or resistant HIV-positive lymphomas have been treated with an autologous peripheral stem cell transplantation (APSCT) in the HAART era. Published data compared favorably with any previous salvage attempt showing a percentage of complete remission ranging from 48% to 90%, and overall survival ranging from 36% to 85% at median follow-up approaching 3 years. However, experiences are still limited and have given somewhat confounding indications, especially concerning timing and patients' selection for APSCT and feasibility and outcome for allogeneic stem cell transplant. Moreover, little data exist on the kinetics of immunological reconstitution after APSCT or relevant to the outcome of HIV infection. The aim of this review is to discuss current knowledge of the role of allogeneic and autologous stem cell transplantation as a modality in the cure of HIV and hemopoietic cancer patients. Several topics dealing with practical aspects concerning the management of APSCT in HIV-positive patients, including patient selection, timing of transplant, conditioning regimen, and relapse or nonrelapse mortality, are discussed. Data relating to the effects of mobilization and transplantation on virological parameters and pre- and posttransplant immune reconstitution are reviewed. Finally, in this review, we examine several ethical and legal issues relative to banking infected or potentially infected peripheral blood stem cells and we describe our experience and strategies to protect positive and negative donors/recipients and the health of caretakers.