Busulfan-cyclofosfamide is one of the conditioning regimens used before HSCT in CML patients. Using cyclofosfamide resulting toxicity and increased mortality. Recently favorable outcomes were seen with Fludarabine. The purpose of the present study is comparing the efficacy of these two regimens in CML in selected patient populations in Shari'ati hospital, Tehran, Iran. The stydy was conducted on CML patients were bone marrow transplanted in 2000-2005. The strategy of this center in one period was using Busulfan-cyclofosfamide and in the other period was Fludarabine-busulfan. All data such as complications and side effects of two regimens, mortality, cause of death and were analyzed in SPSS system and with Kaplan-Meyer methods, regression and chi-square test. P<0.05 were significant. Data of 47 patients in BU/CY group and 17 patients in FLU/BU group respectively were analyzed. Transplantation related mortality (TRM) was 25.5% in BU/CY group and 23.5% in FLU/BU group. The day 100 Overall survival was 4.3% in FLU/BU group but in BU/CY no patient were died (p<0.05). In conclusion, using Fludarabine-busulfan had favorable outcomes than Busulfan-cyclofosfamide regimens.