OBJECTIVE: To analyze the incidence of hemorrhagic cystitis (HC) after allogeneic hematopoietic stem cell transplantation and the factors affecting HC, so as to provide clinical evidence for further treatment of HC. METHODS: The HC of 113 patients after allogeneic hematopoietic stem cell transplantation in Affiliated Hospital of Xuzhou Medical University between the years 2014-2016 was analyzed respectively. All cases of HC were divided into HC group and non-HC(control) group. The follow-up time: from preeonditionig day to 180 d after transplantation. The 10 clinical parameters were selected for univariate analysis with COX regression analysis: sex, age (＜25 years and 25 years), primary disease, conditioning regimen with anti-thymoglobulin(ATG), sex-mismatch in recipients, haploidential HSCT, cytomegalovirus (CMV) viremia, EB viremia, graft-versus-host disease (GVHD), and primary disease relapse, the factors significant at the 0.1 level in univariate analysis should be further evaluated by multivariate analysis using a COX regression analysis. The difference was significant at P＜0.05 in multivariate analysis. RESULTS: The HC occured in 31 of 113 patients (27.4%), with 5 cases of grade I (5.5%), 19 of grade II (16.8%), 5 of grade III (4.4%), and 2 of grade IV (1.8%). The median time of HC onset was 37 days (26-70 d) after transplantation. The median duration of HC was 14 days (5-55d). Univariate analysis showed that conditioning with anti-thymoglobulin (ATG) (RR=6.170, 95%CI: 1.875-20.306, P＜0.01), CMV viremia (RR=7.633, 95%CI：2.318-25.133) (P＜0.01), haploidentical HSCT (RR=0.307, 95%CI：0.137-0.686, P＜0.01), GVHD (RR=1.891, 95%CI：0.918-3.898, P＞0.05) were the risk factors for recovery from HC. The multivatiate analysis of above-mentioned risk factors with statistical significance showed that only CMV viremia (RR=4.770, 95%CI: 1.394-16.326, P＜0.05) was the indentified risk factor affecting the recovery from HC. CONCLUSION: Monitoring CMV viremia and antivirotic treatment are effective measurs to prevent the occurrence of HC and promote the recovery from HC.