The Functional Assessment of Cancer Therapy-Bone Marrow Transplant measures quality of life (QOL) in SCT patients. Prior reports found mixed results regarding QOL differences among autologous and allogeneic SCT patients. In addition, there is a paucity of literature examining differences in QOL patterns over time between autologous and allogeneic patients. The present study examines differences in QOL between patients free of clinical depression undergoing autologous (n = 41) and allogeneic (n = 64) SCT during early stages of treatment. Despite clinical differences, autologous and allogeneic patients demonstrated similar changes in QOL. The exception was the Functional subscale which indicated worse QOL for allogeneic patients at discharge (F test = 4.61, df = 1, P < 0.05); allogeneic patients (Mean = 13.06, s.d. = 5.36) indicated they were less able to function at work and were less accepting of their illness than autologous patients (Mean = 16.02, s.d. = 6.73). There was a significant main effect for time on nearly all QOL subscales (P < 0.05) demonstrating decline during treatment and return to baseline by discharge; only the Social Well-Being scale did not significantly change over time. These results help to understand patients' response to SCT in the earliest stages and ultimately help identify patients at risk who could benefit from therapeutic interventions.