Since 1999, we started to modify the conditioning regimen in allogeneic stem cell transplantation for middle-aged to elderly patients (> = 50), and experimented with 3 conditioning regimens. The clinical outcome was compared between fludarabine/melphalan (FLU/MEL) conditioning and two other conditioning regimens (reduced TBI (7.5 Gy) and BU/CY). From 1999 through 2005, a total of 33 patients aged 50 or more with a hematological malignancy received allogeneic transplantation in our institute. Seventeen received FLU/MEL conditioning and 16 received the other conditioning regimens. The FLU/MEL group included more patients receiving unrelated bone marrow transplantation. There were no differences in primary disease, risk, HLA disparity, GVHD prophylaxis and stem cell source. Sustained engraftment was achieved in all evaluable patients in both groups. Regimen-related toxicities were the same in both groups. Transplant-related-mortality (TRM), relapse rate and disease-free survival were 22% and 25%, 25% and 47%, 59% and 37% in the FLU/MEL group and in the other group, respectively. The incidence of grade II-IV acute GVHD was 25% and 13%, respectively, and that of chronic GVHD was 38% and 56%, respectively. FLU/MEL conditioning achieved satisfactory engraftment. Although the relapse rate showed a lower tendency with FLU/MEL conditioning, there were no differences as far as TRM was concerned. FLU/MEL conditioning could be a novel conditioning regimen for middle-aged to elderly patients.