BACKGROUND Polyomavirus infection is common in childhood, with a seroprevalence of 60% to 100%. These viruses remain latent mostly in the kidney. Impairment in cellular immunity can allow reactivation of the virus. Reactivation can occur in 10% to 45% of renal allografts. A higher intensity of immunosuppression and the allogeneic microenvironment of the graft have been suggested to predispose to reactivation. There are limited data on the status of viral activity in the native kidneys of non-renal solid organ recipients. METHODS Thirty-eight recipients of pancreas transplant alone were evaluated for evidence of polyomavirus reactivation by urine cytology. All had received induction therapy and were maintained on tacrolimus, mycophenolate mofetil, and prednisone. The renal function and degree of exposure to immunosuppressive agents of patients shedding polyomavirus-infected renal tubular cells were compared with those of patients with negative urine cytology. RESULTS Screening cytology was performed 16 months (mean) after transplantation. Four subjects (11%) had polyomaviruria. The renal function at baseline and time of screening was comparable between the two groups. The 12-hour trough levels of tacrolimus were significantly higher in patients with positive cytology compared with those without viruria. The doses of mycophenolate mofetil and prednisone were not different between the two groups. CONCLUSIONS This study shows that polyomavirus reactivation in native kidneys and urinary tract of pancreas transplant alone patients is not uncommon. In these recipients, viral reactivation was not associated with significant renal functional impairment. The results also suggest that patients who are exposed to higher blood levels of tacrolimus are at higher risk of viral reactivation.