Lymphoma remains a leading cause of mortality in HIV-infected patients. In the HIV-negative setting, high-dose therapy with autologous stem cell transplantation has been a long accepted treatment for certain malignancies such as lymphoma and leukemia. Early transplant trials excluded older patients and patients with comorbidities such as HIV infection. The procedure-related mortality of transplantation, however, has decreased both due to the use of peripheral blood stem cells instead of bone marrow and due to the use of new reduced intensity conditioning regimens. During this same era, the treatment of HIV infection has also become more effective. Patients are no longer dying of opportunistic infections and in addition, their hematologic function has improved. With these advances in HIV therapy, it is possible for HIV-infected patients to mobilize an adequate number of stem cells for an autologous transplant. In addition, with appropriate antiretroviral therapy and infection prophylaxis, the HIV-infected patient can tolerate intensive doses of chemotherapy. This review will summarize clinical trials of autologous stem cell transplantation in HIV-positive patients. Furthermore, the field of solid-organ transplantation has grown to also include HIV-positive patients. The challenges in solid-organ transplantation are similar to allogeneic stem cell transplantation, namely that patients require chronic immunosuppression. This article will also review some of the approaches to allogeneic stem cell transplantation in the HIV-positive patient and provide a rationale for the broader use of stem cell transplantation for appropriate HIV-related hematologic malignancies.