Objective: To evaluate the alterations in coagulation in patients during conditioning with modified busulfan plus cyclophosphamide (BU/CY) +/- antithymocyte globulin (ATG) regimen before allogeneic hematopoietic stem cell transplantation (allo-HSCT), and to assess the effect of ATG on coagulation system., Methods: Thirty-five patients with various hematological malignancies undergoing allo-HSCT were assessed. Of them, 19 patients with HLA-matched sibling donors (group A) were conditioned with modified BU/CY regimen, 16 with HLA-mismatched family members or HLA-matched unrelated donors (group B) were conditioned with modified BU/CY + ATG regimen. Blood samples were collected before the beginning of conditioning till d + 1 after allo-HSCT. The following parameters were measured: prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen (Fg), antithrombin (AT), D-Dimer, fibrin degradation product (FDP), platelet (BPC), liver enzymes and bilirubin. FVIII: C, FIX: C, FXI: C and FXII: C in prolonged APTT blood samples were also determined. Clinical hemorrhagic symptoms were monitored., Results: During conditioning, temporary lengthening of APTT, persistent rising in Fg and declining of BPC were observed in the two groups. Alterations of Fg and BPC were more significant in group B than in group A. Transient D-Dimer increase occurred only in group B on administration of ATG. Among intrinsic pathway coagulation factors, FXII: C and FXI: C were commonly decreased while APTT prolonged. No difference between the two groups was found with regard to PT, FDP, AT and liver parameters which remained in normal ranges. Most of patients in the two groups did not have overt bleeding manifestations., Conclusions: Modified BU/CY +/- ATG conditioning regimen can induce subclinical alterations in coagulation. The regimen containing ATG has more significant effect on coagulation parameters.