Objective To evaluate efficacy and safety of a novel prevention regimen for acute graft versus host disease (aGVHD) with low-dose cyclophosphamide in place of methotrexate. Methods From January 2013 to May 2015, a total of 75 patients with hematological diseases underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) in Department of Hematology, Sichuan Provincial People′s Hospital were selected as study subjects. Among them, 43 patients received related matched allo-HSCT, 32 patients received haploidentical allo-HSCT. According to different regimens of aGVHD prevention, study subjects were divided into study group (n=32) who received a novel aGVHD prevention regimen with low-dose cyclophosphamide combined with cyclosporine A and mycophenolate mofetil, and control group (n=43) who received a classic aGVHD prevention regimen with methotrexate combined with cyclosporine A and mycophenolate mofetil. The constituent ratio of gender, age, constituent ratio of different diseases, constituent ratio of different allo-HSCT types, the time of neutrophil and platelet engraftment, incidences of aGVHD and chronic graft versus host disease (cGVHD), incidences of oral mucositis associated with transplantation and hemorrhagic cystitis (HC), recurrence rate, overall survival (OS) rate between two groups were analyzed retrospectively, and compared statistically. The study protocol was approved by the Ethical Review Board of Investigation in Human at Sichuan Provincial People′s Hospital. Informed consents were obtained from all participants. Results ①There were no significant differences in constituent ratio of gender, age, constituent ratio of different diseases and constituent ratio of different allo-HSCT types between two groups (P>0.05). ② All patients achieved hematopoietic stem cell engrafted, complete chimerism states after allo-HSCT, and obtained hematopoietic reconstitution. Time of neutrophils engraftment of patients in study group and control group were (13.9±1.6) d and (14.6±1.2) d, respectively. There was no significant difference in time of neutrophils engraftment between two groups (t=0.559, P=0.606). Time of platelet engraftment of patients in study group and control group were (15.1±1.3) d and (17.2±1.4) d, respectively. There was no significant difference in time of platelet engraftment between two groups (t=1.512, P=0.374). ③ Among patients received related matched allo-HSCT, there was no significant difference in incidence of gradeⅠ-Ⅳ aGVHD between two groups within 100 d after allo-HSCT (χ2=0.135, P=0.447). And there were no significant differences in incidences of gradeⅠ-Ⅱ and Ⅲ-Ⅳ aGVHD of patients received related matched allo-HSCT between two groups (χ2=0.157, 0.254; P=0.776, 1.328). At end of the follow-up, there were no significant differences in incidences of localized and extensive cGVHD of patients received related matched allo-HSCT between two groups (χ2=0.018, 1.342; P=0.264, 0.327). Among patients received haploidentical allo-HSCT, there was no significant difference in incidence of gradeⅠ-Ⅳ aGVHD between two groups within 100 d after allo-HSCT (χ2=1.316, P=0.283). And there were no significant differences in incidences of gradeⅠ-Ⅱ and Ⅲ-Ⅳ aGVHD of patients received haploidentical allo-HSCT between two groups (χ2=1.472, 1.087; P=0.296, 0.379). At end of the follow-up, there was no significant difference in the incidence of localized and extensive cGVHD of patients received haploidentical allo-HSCT between two groups (χ2=1.312, 1.129; P=0.287, 0.284). ④ The incidence of oral mucositis associated with transplantation in study group was 29.3% (9/32), which was lower than that in control group (75.6%, 32/43), and the difference was statistically significant (χ2=7.26, P=0.008). The incidence of oral mucositis was only 12.6% (4/32) in study group, and that was 52.8% (23/43) in control group. ⑤There was no significant difference in incidence of HC between two groups after allo-HSCT (χ2=0.596, P=0.142). ⑥ There was no significant difference in recurrence rate and OS rate between two groups at the end of follow-up (χ2=1.317, 0.115; P=0.281, 0.734). Conclusions The novel aGVHD prevention regimen of low-doses cyclophosphamide in place of methotrexate not only has a prophylactic effect of aGVHD similar to that of classic aGVHD prevention regimen, ensures hematopoietic reconstitution, but also significantly reduces incidence of transplant-associated oral mucositis without increasing incidence of HC. Wether the novel aGVHD prevention regimen of low-dose cyclophosphamide in place of methotrexate after allo-HSCT can be used as an alternative to the classic aGVHD prevention regimen requires multicenter, large sample randomized controlled trials to further study and confirm. Key words: Cyclophosphamide; Hematopoietic stem cell transplantation; Graft vs host disease