Abstract Background and Aims Infection of the renal allograft by Polyomavirus BK (BKV) causes tubular cell injury and interstitial inflammation, which leads to subsequent interstitial fibrosis and tubular atrophy (IFTA). The presence and degree of inflammation within these areas (i-IFTA) is associated with worse outcomes in kidney transplant (KT) patients. The aim of this study was to investigate the association between BKV viremia and viruria and the presence of IFTA and i-IFTA, decline of renal function, and graft loss. Method We conducted a single-center retrospective case-control study, which included all patients who underwent an allograft biopsy between January 2018 and December 2022. All biopsies were made for-cause (allograft dysfunction with increased serum creatinine). Real-time polymerase chain reaction was used to detect and quantitate BK viral load in serum and urine samples. Patients were included if they had at least 6 months since KT and if they had serial evaluation of BKV viremia and viruria previously to the biopsy. We evaluated, in the graft biopsy, the percentage of IFTA, and also i-IFTA. Estimated glomerular filtration rate (eGFR) was obtained at baseline and 1 year after the biopsy. Graft loss was evaluated at 6 months and 1 year after the biopsy. Results Mean age of the population was 53,5 years and 67% were males. A total of 116 biopsies were performed during the studied period and 72 met the inclusion criteria. Ten percent of patients developed persistent (≥ 3 months) BKV viremia, 24% developed persistent BKV viruria, and 18% developed persistent JCV viruria. Five cases of polyomavirus-associated nephropathy were diagnosed. The other most common diagnoses were T cell-mediated rejection (24%), antibody-mediated rejection (15%), and focal segmental glomerulosclerosis (15%). In patients with persistent BKV viremia, a higher viral load had a strong positive association with the degree of i-IFTA (r=0.954; P = .001). Patients with BKV viremia and/or viruria were more likely to present more severe IFTA (≥ 40%) and i-IFTA (grade ≥2) in allograft biopsy (P = .03). Patients with higher degrees of IFTA and i-IFTA were more likely to experience graft loss 1 year after the biopsy (P = .01). There was no significant association between the presence of BKV viremia and/or viruria and the decline of eGFR, nor with the incidence of graft loss 1 year after the biopsy. In multivariable analysis adjusted for age, eGFR at the time of biopsy, the presence of donor-specific antibodies and the main diagnosis of allograft biopsy, the presence of BK viremia and/or viruria was a significant predictor of more severe IFTA and i-IFTA (P = .04). Conclusion In our population, higher BK viremia loads were associated with more extensive inflammation within areas of IFTA. Patients with BK viremia and/or viruria, independently of the main diagnosis of the biopsy, were more likely to exhibit more severe IFTA and i-IFTA in allograft biopsies, but no association with the incidence of dialysis at 1 year was shown. Longer prospective studies are needed to investigate whether BKV infection treatment/ reduction of immunosuppression can slow down fibrosis progression and minimizes i-IFTA.