Abstract Reactivation of BK virus (BKV) can occur during intensive immunosuppression such as in allogenic hematopoietic stem cell transplant (AHSCT) recipients for whom a systematic PCR urine test for BKV will be positive in 50% to 100% of patients. Only 5% to 40% will develop BKV hemorrhagic cystitis (HC). Thus, BKV PCR testing is useful to confirm a diagnosis of BKV‐HC but not to predict its occurrence. The aim of this retrospective study was to ascertain the risk factors of developing BKV HC, mostly in patients receiving posttransplant cyclophosphamide. The study looked at data from Grenoble Alpes University Hospital included in the national retrospective register ProMISe, administered by the “Société Francophone de Greffe de Moelle et de Thérapie Cellulaire”. Urine BKV PCR was performed when patients presented grade ≥ 2 hematuria with clinical symptoms of cystitis. BKV‐HC was defined as an association of clinical symptoms of cystitis, grade ≥ 2 hematuria and BKV viruria > 7 log 10 copies/ml. From January 2014 to January 2018, 168 AHSCTs were considered for analysis, of which 43 (25.6%) developed BKV‐HC and 44.9% of the subgroup that received posttransplant cyclophosphamide. After logistic regression, the risk factors associated with BKV‐HC were reduced to posttransplantation exposure to cyclophosphamide (OR 4.25, [1.66; 10.87], P = .02), age < 40 y (OR 3.85 [1.51; 9.80], P = .005) and corticosteroid therapy (OR 3.86, [1.59; 9.36], P = .003). Exposure to cyclophosphamide, younger age (<40) and corticosteroid therapy are potential risk factors for BKV‐HC.