Post-transplant Cyclophosphamide (PT-Cy) has proved efficacy as GVHD prophylaxis regimen after HSCT. However, experiences are limited with controversial results. We herein, assess the efficacy of PT-Cy compared to Methotrexate regimen. Eighty patients with acute leukemia received a fully matched allogeneic HSCT or a Haplo-identical HSCT were analyzed. Group I (Historical group) included 40 patients received Methotrexate, Cyclosporine and MMF. They were transplanted with fully matched allogeneic transplantation. Group II included 40 patients received PT-Cy, Cyclosporine and MMF. They were subdivided to 2 subgroups. Subgroup IIA included 22 patients received fully matched allo- HSCT and subgroup IIB included 18 patients received Haplo- HSCT. Group IIA showed significantly lower incidence of cGVHD when compared to group I with an incidence of 22.7% and 67% respectively (P = 0.002). Group IIA was associated with reduced risk of extensive cGVHD compared to MTX group (P =0.003). No significant differences were found in the incidence of aGVHD, relapse rates, relapse or non-relapse related mortalities, OS and DFS data among the different groups (P>0.05). In conclusion, PT-Cy with addition of IS drugs has statistically significant difference in reducing the incidence of cGvHD in both fully matched and Haplo SCT with less hepatic and renal toxicity.