BACKGROUND: Human cytomegalovirus (CMV) infection is associated with inferior survival in renal transplant patients, and ganciclovir (GCV) prophylaxis is associated with improved survival. In a murine CMV (MCMV) renal transplantation model, ganciclovir prophylaxis improved innate infiltrates and allograft damage during the period of prophylaxis. In this study, late effects were examined after the discontinuation of prophylaxis. METHODS: MCMV D+/R-and D-/R-allogeneic transplants were performed with cyclosporine immunosuppression. One D+/R-cohort received ganciclovir prophylaxis for 14 days after transplantation followed by 28 days without ganciclovir. At 42 days after transplantation, grafts were analyzed for histologic tissue damage and immune infiltrates. Another D+/R-cohort was treated with anti-NK1.1 antibodies for 14 days after transplantation and compared with animals without natural killer (NK) cell depletion. RESULTS: At day 42, MCMV-infected transplants had higher damage scores (15.6±0.6) compared with uninfected transplants (8.3±0.9; P<0.01), which improved in ganciclovir-treated allografts (9.5±1.4). MCMV-infected grafts contained greater frequencies of NK cell and myeloid infiltrates compared with uninfected grafts (P<0.05), which decreased in the ganciclovir-treated grafts. NK cell depletion improved allograft histology of MCMV-infected grafts. CONCLUSIONS: MCMV infection exacerbates late renal allograft damage and is associated with NK and myeloid cell infiltrates. Ganciclovir prophylaxis reduces allograft injury and NK cell and myeloid infiltrates even after the cessation of prophylaxis. NK cell depletion in MCMV-infected transplants also improves histology. These results suggest that ganciclovir prophylaxis may have a long-term beneficial effect on CMV-infected renal allografts and suggest a potential role for NK cells in the pathogenesis of CMV-associated allograft injury. © 2012 Lippincott Williams & Wilkins.