Primary central nervous system lymphoma (PCNSL) is a rare B-cell lymphoid neoplasm for which current regimens utilizing standard-dose chemotherapy and/or radiation therapy lead to high relapse rates and/or unacceptable neurologic sequelae. High-dose chemotherapy followed by hematopoietic stem cell transplantation may overcome limitations of current treatment schemas. A search was performed of all English-language literature (1968 to June 2009) within the MEDLINE, EMBASE and Cochrane Library databases to identify relevant clinical trials using the terms stem cell transplantation, bone marrow transplantation, primary central nervous system lymphoma, and PCNSL. Bibliographies were reviewed to extract other relevant articles. Use of high-dose chemotherapy followed by hematopoietic stem cell transplantation for the treatment of PCNSL in a predominantly elderly population is feasible. Use of this treatment modality for newly diagnosed and recurrent or relapsed disease is burdened by a paucity of data guiding patient selection, optimal induction regimen, stem cell mobilization and conditioning chemotherapy. Data are also sparse and confounding regarding timing of initiation of this procedure relative to the natural history of the disease and timing of each chemotherapy regimen relative to each other. High-dose chemotherapy followed by hematopoietic stem cell transplantation remains an experimental procedure with insufficient data to guide clinicians. However, the data are encouraging and merit continued research to guide patient selection and treatment regimens which may produce optimal outcomes.