Hemorrhagic cystitis (HC) is an important cause of morbidity and mortality in Bone Marrow Transplant (BMT) recipients. HC presentations are classified to early and late onset and one of the causative agents of HC late onset is viral infections. In this research for measuring the role Adenovirus (ADV) infections in late onset of HC, the prevalence of this viral infection in BMT recipients were determined .Also the role of another risk factors including: hematological and biochemical characteristics, clinical conditions, grade of GVHD in HC presentations were determined. We cohort and retrospectively studied 30 and 24 BMT recipients and donors respectively. The number of 293 EDTA treated blood samples and 293 urine samples were collected from BMT recipients and donors. One sample was collected pre-transplantation from BMT recipients and donors and also one sample per week for 100 days from BMT recipients post-transplantation ADVmonoplex in house PCR were proceed for determination of these viral prevalence in HC incidence in BMT patients. Also all the data of this investigation were statistically analyzed with version 12 of SPSS. The median incidence of HC in BMT recipients with measurement the grade of HC and with sonographic records of bladder bleeding were 53.3% and 36.7% respectively. Significant correlations were found between ADV-PCR positive results with HC presentation. Significant correlations were detected between hematological characteristics like; WBC count and platelet count and also biochemical characteristics include; cratinin, direct bilirubin and total bilirubin, with ADV-PCR positive results and HC presentation. For significant correlations of HC clinical presentations with positive results of ADV-PCR and also with results of hematological and biochemical tests, monitoring of this viral and biological indexes have a critical role in management of preventive and therapeutic protocols for HC disorder in BMT recipients