The cost-effectiveness of autologous peripheral blood stem cell transplantation (PBSCT) compared with autologous bone marrow transplantation (ABMT) for refractory or relapsed non-Hodgkin's lymphoma (NHL) or Morbus Hodgkin (MH) was assessed. Costs were determined from the induction chemotherapy regimen up to 3 months after discharge from hospital following the transplantation. Quality of life was measured by the EuroQol, the Rotterdam Symptom Checklist (RSCL) and the SF-36. Patients were randomised according to a 2:1 ratio to undergo either PBSCT or ABMT. 62 patients underwent PBSCT and 29 ABMT. Costs of the transplantation period were significantly lower in the PBSCT group (15008 Euros) than in the ABMT group (19000 Euros). Significant differences in quality of life were all in favour of PBSCT and emerged using the RSCL, both on 14 days after the transplantation and three months after discharge. We conclude that PBSCT is associated with lower costs and a better quality of life than ABMT for patients with refractory or relapsed NHL or MH.