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Allogeneic peripheral blood stem cell transplantation (alloPBSCT) is an emerging technology. As this technology develops, transplant centers are concerned with looking for technologic advances that will result in improvements in clinical outcomes and lower costs. We provide comparative estimates of costs and resource use for alloPBSCT in comparison to allogeneic bone marrow transplantation (alloBMT) for persons with hematologic malignancies from the time of harvest to 100 days post transplant. A retrospective, cost-identification analysis was conducted for patients in two consecutive phase II clinical trials at the University of Nebraska Medical Center. Identical preparative regimens, graft-versus-host disease prophylaxis, post-transplant hematopoietic colony-stimulating factor treatment regimens, and discharge criteria were used. Total median costs were $18,304 lower for alloPBSCT, with lower costs during recovery; specifically for hospitalization, platelet products, hematopoietic growth factors, intravenous hyperalimentation, supportive care agents, supplies, and antibacterial agents. This study provides preliminary evidence for short-term cost savings associated with alloPBSCT. However, concerns exist over the potential for higher costs due to preliminary reports of higher rates of chronic graft-versus-host disease, as well as more intensive induction regimens that may result in lower relapse rates. The premature adoption of new technologies based on short-term economic factors, in the absence of adequate clinical trial data, may prove to be ill-advised, particularly for complex medical treatments such as allogeneic transplantation.