The total cost of hematopoietic stem cell transplantation (HSCT) as well as the financial impact of HSCT on the house holds of patients have been elusive. Between 2005 and 2012, we analyzed 191 HSCT in adult patients with leukemia with reduced-intensity conditioning (RIC) regimen (n = 79) and with myeloablative conditioning (MAC) regimen (n = 112). The direct medical costs were calculated from healthcare claims obtained from the Seoul National University Hospital, and the direct non-medical and the indirect costs were calculated from national statistics. The mean direct medical cost was $55,039, direct non-medical cost was $6394, and indirect cost was $7503 from transplantation to one yr after transplantation in the RIC group and $72,916, $6993, and $9057 in the MAC group, respectively, based on the exchange rate of Korean won 1060 = US$1. The total costs for one yr were $68,938 and $88,967, constituting for 273% and 357% of the per capita income, respectively. The total costs, direct medical costs, and indirect costs showed statistically significant differences (p = 0.006, p = 0.007, and p = 0.017). No significant differences were found for leukemia-free survival and overall survival. RIC-HSCT provides lower costs within the first year of transplantation with comparable long-term clinical outcomes.