High-dose therapy and autologous stem cell transplant (HDT-ASCT) is the standard of care for relapsed and refractory diffuse large B cell lymphoma and Hodgkin's lymphoma; however, the role for HDT-ASCT in the treatment of follicular lymphoma (FL), mantle cell lymphoma (MCL), and peripheral T cell lymphoma (PTCL) is controversial. In FL, phase II and randomized data support the use of HDT-ASCT in the relapsed setting and incorporation of rituximab into mobilization regimens and post-transplant maintenance appears to prolong remission durations. Allogeneic stem cell transplant remains the only curative treatment option and is appropriate for patients with high bone marrow disease burdens and refractory disease. In MCL, HDT-ASCT is most often administered up front, and phase II studies using intense immunochemotherapy followed by HDT-ASCT in first complete response (CR) have shown the most impressive outcomes. Complicating the situation, however, are data supporting up-front intensive immunochemotherapy without HDT-ASCT consolidation as well as a "watch and wait" strategy for selected patients. Finally, in PTCL, phase II data support treatment with HDT-ASCT in first CR, and it is rarely appropriate in the relapsed setting. Furthermore, disease status at the time of transplant likely impacts outcome; however, this needs to be evaluated further. Overall, HDT-ASCT is an important element of the treatment of relapsed FL and untreated MCL and PTCL; however, large prospective studies are needed to confirm its role and identify the most optimal induction, mobilization, and maintenance regimens for each disease.