BACKGROUND: Hemorrhagic cystitis(HC), a common complication of bone marrow transplantation(BMT), is known to be associated with toxic metabolites of chemotherapy drugs or reactivation of primary virus infections. In this study, we evaluated the association between polyomaviruria and HC in BMT patients. METHODS: Urine specimens of 29 patients with HC after BMT were requested for the detection of polyomavirus by culture and polyomerase chain reaction(PCR). Several clinical parameters were analyzed in relations to the presence of polyomaviruria. For comparison, 19 patients without HC after BMT were involved in this study. RESULTS: Overall, 45 of 558 patients developed HC after BMT, and the incidence of HC was estimated to be 8.1%. Patients group showed significantly high prevalence of BK viruria compared with control group by PCR(72.4% vs 31.6%, P = 0.005). In patients group, BK virus was isolated in 44.8%(13/29) by culture and detected in 72.4%(21/29) by PCR. Results of both methods were agreed in 65.5%(19/29). JC virus was detected in 6.9%(2/29) by PCR. Sex, conditioning regimen, graft-versus-host disease(GVHD), onset time after BMT and duration of hematuria did not show any statistically significant differences between the two groups based on the presence of BK viruria by PCR. CONCLUSIONS: High prevalence of BK viruria in HC patients after BMT suggests the possible association between BK virus and HC. However, we could not find any significant clinical parameters in association with BK viruria.