Polyomavirus-induced nephropathy has emerged as an important cause of renal graft dysfunction. Limited pediatric data are available for this disease. We therefore reviewed the results of the first year of polyomavirus screening in our pediatric renal transplant recipients to determine the prevalence of polyomavirus viremia and urinary shedding. Screening included detection of polyomavirus in plasma by polymerase chain reaction (PCR) and in urine by electron microscopy (EM). In patients with a positive screening test, an assessment of graft dysfunction was made. Fifty-two patients met the inclusion criteria. Urinary EM was performed in 205 samples and polyomavirus was detected in 10 patients, representing 19% of the study population. PCR was performed on 222 samples and was positive for the BK virus in plasma from seven patients or 13.4% of the study population. Eight patients had a positive screening test and increased creatinine. All these patients underwent renal transplant biopsy. This revealed evidence of polyomavirus nephropathy in four patients. Our findings reveal a high prevalence of polyomavirus in both urine and plasma that is frequently associated with graft dysfunction. These findings support the routine screening of pediatric post-renal transplant patients for polyomavirus replication.