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Polyomavirus BK(BKV) is the cause of polyomavirus‐associated nephropathy resulting in premature graft loss. There are limited data regarding the role of cytomegalovirus (CMV) infection and its prevention in developing BKVviremia and PVAN. In a prospective study, we analyzed 207 consecutive renal transplant recipients previously enrolled in 2 randomized trials evaluating different CMVprevention regimens with routine screening for BKVand CMV. Of these, 59 received valganciclovir and 100 valacyclovir prophylaxis; 48 patients were managed by preemptive therapy. At 3 years, the incidence of BKVviremia and PVANwas 28% and 5%, respectively. CMV DNAemia developed in 55% and CMVdisease in 6%. Both BKVviremia (42% vs 23% vs 21%, P= .006) and PVAN(12% vs 2% vs 2%, P= .011) were increased in patients treated with valganciclovir prophylaxis compared to valacyclovir and preemptive therapy. Using multivariate Cox proportional hazard regression, valganciclovir prophylaxis was independent predictor of BKVviremia (hazard ratio [HR] = 2.38, P= .002) and PVAN(HR= 4.73, P= .026). In contrast, the risk of subsequent BKVviremia was lower in patients with antecedent CMV DNAemia (HR= 0.50, P= .018). These data suggest valganciclovir prophylaxis may be associated with increased risk of BKVviremia and PVAN. CMV DNAemia did not represent a risk for BKV. A post hoc analysis of two randomized trials evaluating CMV prevention strategies in kidney transplant recipients suggests an association between valganciclovir prophylaxis and an increased risk of polyomavirus BK viremia and polyomavirus‐associated nephropathy compared to other modalities, such as high‐dose valacyclovir prophylaxis or a pre‐emptive therapy approach. See the editorial by Pape on page 2401.