Abstract: Objective 　To study and profile human polyomavirus ( HuPV) reactivation after hematopoietic stem cell t ransplantation ( HSCT) . Methods 　Continuously collected middlesteam urine samples from 41 patients with hematopoietic stem cells transplantation and 10 immunocompetent peoples as control group.HuPV DNA was detected with Real-Time PCR and the stains of BK virus and JC virus were distinguished with seminested PCR. Results 　33 of the 41 (80 %) patients shed viruria after HSCT. Of them, 15 (45 %) cases shed BK viruria, 3 (9 %) cases for JCV and 11 (33 %) cases embraced two viral stains that simultaneously or separately in the urinary specimens. The viral stains were not identified in 4 (12 %) cases. Comparison in 26 patients with the initial specimens prior to transplantation subject s that the incidence of viruria is significant increased af ter HSCT ( P < 0. 0001) . Conclusion 　The amount of patients shedding HuPV in urine is significantly increased after HSCT. The impact factors remain ambiguous and the associated clinical significance should be further explored.