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Background: BK virus belongs to the polyomaviridae family. It has been reported that up to 80% of normal population change to seropositive status between 5 and 10 years of age. It has been assumed that the rate of multiple virus isolation is significantly greater in children with acute lymphoblastic leukemia (ALL) than normal population. Considering the scarce data on the presence of urinary excretion of BKV in children with ALL, we studied the urine BKV in newly diagnosed leukemic children comparing with normal population. Methods: 62 subjects (31 all cases and 31 controls) were enrolled in the study. Epitelial cells isolated from urine samples were screened for the BKV DNA with PCR method. Finding: Positive PCR for urine BK virus was seen in 3 children (9.7%). No positive result for urine BKV was achieved in control group. However, Fisher Exact test did not show any significant difference between two groups (P > 0.05). In addition, there was no significant correlation between BKV positivity and frequency of relapses. Furthermore, the mean time of diagnosis was not different between BKV positive and negative groups. Conclusion: In our study there was not any significant difference between BK viruria in ALL children and control group, no case of BK viruria had been found in control group. To demonstrate the role of BKV in inducing ALL or increasing number of relapses, prospective studies on larger scale of population and evaluating both serum and urine for BKV are recommended.