The aim of this study was to analyze the risk factors of hemorrhagic cystitis (HC) after hematopoietic stem cell transplantation (HSCT). The data of 188 transplant patients treated from July 2003 to August 2009 in Peking University First Hospital were studied. The patients were followed up to 180 days after HSCT. Clinical records of the total 188 cases and the 150 cases underwent allogeneic HSCT out of 188 cases were analyzed by using a Cox regression model respectively. The results indicated as follows: (1) 51 of 188 patients developed HC (27.12%). Univariate analysis showed that sex (male RR = 1.673, p = 0.076), allogeneic HSCT (RR = 1.848, p = 0.061) were related to HC, and allogeneic HSCT (RR = 4.508, p = 0.037) was the independent risk factor for HC by multivariate analysis. (2) HC occurred in 32.67% (49/150) patients who underwent allogeneic HSCT, with 42 cases of grade II-IV HC (28.00%). For the incidence of grade II-IV HC, univariate analysis revealed mismatched related donor/matched unrelated donor (RR 2.444, p = 0.018), CMV viruria (RR 2.059, p = 0.021) and CMV positive in serum and urine at the same time (RR 2.497, p = 0.003) were risk factors. The following factors, as conditioning with Fludarabine (Flu) (RR 0.504, p = 0.059) and TBI (RR 0.185, p = 0.095), were associated with a decreased tendency of II-IV HC at age of 26 - 40 (compared with age ≤ 25 or ≥ 41, RR 0.454, p = 0.056). Some others, as conditioning with CTX (RR2.015, p = 0.063), the application of ATG (RR 2.343, p = 0.054) and CMV viremia (RR 2.123, p = 0.088), were associated with an increased tendency of II-IV HC by univariate analysis. Multivariate analysis demonstrated that CMV positive in serum and urine at the same time (RR 2.269, p = 0.008), conditioning without Flu (RR = 2.106, p = 0.040) were the independent risk factor for grade II-IV HC. And the application of ATG (RR = 2.154, p = 0.083) was related to the tendency of higher incidence of grade II-IV HC. It is concluded that the incidence of HC is high in patients underwent allogeneic HSCT. CMV positive in serum and urine at the same time, while conditioning without Flu are the independent risk factors of grade II-IV HC. Application of ATG is related to the increased trend of grade II-IV HC.