In hematologic malignancy patients undergoing allogeneic HSCT, the optimal conditioning regimen is uncertain and comparative studies of conditioning regimens with each other are needed. In the current study, it was intended to compare the toxicity profile of two myeloablative conditioning regimens (treosulfan-fludarabine vs busulfan-cyclophosphamide) and their effects on clinical outcomes. The data of patients who underwent allogeneic HSCT between 2015 and 2020 in Inonu University Turgut Ozal Medical Center were retrospectively analyzed. Patients receiving treosulfan-fludarabine (treosulfan group) or busulfan-cyclophosphamide (busulfan group) as a conditioning regimen prior to allogeneic HSCT were matched 1:1 according to their disease and age. A total of 42 patients were included in this trial (busulfan:21, treosulfan:21). The mean age of the patients was 45.2±14 years, and regimen-related toxicities and clinical outcomes of both groups were similar (all p>0.05). The median follow-up time of the patients in the treosulfan regimen groups was 9 months, while it was 15 months in the busulfan regimen group (p=0.82). 54.8% of the patients (12 treosulfan, 11 busulfan) died after a median follow-up of 9.5 months. When the effects of the two conditioning regimens on were compared in 28 acute myeloid leukemia (AML) patients, the engraftment times, acute and chronic graft versus host disease incidences, and sinusoidal obstruction syndrome incidence were found to be similar in busulfan and treosulfan groups (all p>0.05). In addition, the estimated median progression-free survival (p=0.938) and overall survival (p=0.672) of the groups were similar. Treosulfan-fludarabine appears to be a conditioning regimen that can be used as an alternative to busulfan-cyclophosphamide. Prospective randomized studies are needed to confirm the data in our study.