The present study aimed to follow-up variations in plasma Flt3 ligand (FL) concentration after hematopoietic stem cell transplantation and to compare the influence of conditioning regimens on variations in FL concentration. Ten patients undergoing a conditioning regimen, including BEAM, cyclophosphamide (Cy) + total body irradiation or Cy + anti-thymocyte globulins (ATG), which was then followed by hematopoietic stem cell transplantation, were studied. Plasma FL concentrations, white blood cell (WBC) expression of both FL mRNA and the membrane-bound form of FL were carried out at different times post-treatment. The results indicated that plasma FL concentration increased rapidly after the conditioning regimen in all patients, in correlation with the decrease in number of WBCs. The area under the curve of FL according to time was directly correlated with the duration of pancytopenia, except when ATG was included in the conditioning regimen. Although the number of patients was limited in this study, the comparison of ATG-treated patients and other patients suggests that plasma FL concentration is regulated by a complex mechanism partly involving circulating blood cells.