Stem-cell transplantation (SCT) has become the treatment of choice for patients with relapsed aggressive non-Hodgkin's lymphoma (NHL). However, the role of SCT in the management of patients with indolent NHL remains controversial. Indolent follicular lymphomas are diseases which are generally incurable with conventional therapy. Although patients can survive for prolonged periods, the median duration of first remission is approximately 3 years, and subsequent remissions are progressively shorter with time. Emerging evidence suggests that high-dose chemotherapy with SCT leads to prolonged disease-free and overall survival in a subset of patients with indolent NHL. However, there is increasing concern regarding the toxicity of SCT, especially the long-term risk of developing myelodysplastic syndrome. It is still unclear as to when this approach should be used. Poorer outcomes have been obtained in heavily pretreated patients but encouraging results are being reported for patients undergoing SCT early during the course of their disease. Investigators are now focusing on how to improve SCT efficacy in order to eradicate minimal residual disease. Many ongoing studies are especially exploring the impact of stem-cell purging and novel ablative regimens combined with allogeneic transplantation.