Herein reported is a severe case of BK virus nephropathy, probably caused by an intense/overimmunosuppression and identified 17 months after transplantation. The diagnostic biopsy showed extracapillary proliferation and typical cytopathic lesions, both in tubular epithelial cells and in those of the glomerular crescents. Severe inflammatory infiltrates, tubulitis, tubular atrophy and fibrosis were also observed. Immunohistochemistry and molecular biology disclosed the presence of an AS variant of the BK virus with a high viral load, both in renal tissue and urine. Immunosuppression was reduced and Leflunomide therapy administered for a month. Although this led to an improvement in the renal function, the therapy had to be suspended due to the onset of a skin rash. A second biopsy was performed 7 months later. The cellular crescents were no longer present and there was no evidence of either histologic or immunohistochemical findings consistent with an active BK virus infection. Tubular atrophy and interstitial fibrosis were still present. In addition, fibrotic crescents, which may be interpreted as late scarring changes of previous epithelial proliferation, were found. Although molecular investigation still showed the presence of the BK virus, the viral load in renal tissue, urine and serum was greatly reduced. Indeed, serum and urine viral load was still low at the last control, five months after the second biopsy. The morphologic and clinical evolution are reported and the possible role of the therapy is discussed.