Despite the high cure rates achieved with intensified primary therapies for childhood non-Hodgkin's lymphomas (NHL), the prognosis for children with relapsed or refractory disease is poor. Optimal treatment for this group remains a challenge. Dose intensification followed by stem cell transplantation has been used in these circumstances and may provide a curative treatment option for these patients, but the number of children treated using this approach is relatively small and its effectiveness has been difficult to judge. Moreover, the limited experience is insufficient to define the patient most likely to benefit from transplantation. Likewise, the selection of autologous or allogeneic transplantation and the optimal conditioning regimen are debated. We summarize the current experience for stem cell transplantation in childhood NHL and offer our recommendations.