Persisting polyomavirus replication is now widely recognized as a (re-)emerging cause of renal allograft dysfunction. Up to 5% of renal allograft recipients can be affected about 40weeks (range 6-150) post-transplantation. Progression to irreversible failure of the allograft has been observed in up to 45% of all cases. The BK virus strain is involved in the majority of the cases. Risk factors may include treatment of rejection episodes and increasing viral replication under potent immunosuppressive drugs such as tacrolimus, sirolimus or mycophenolate. The diagnosis requires the histological demonstration of nuclear polyomavirus inclusions in affected tubular epithelial cells. Interstitial inflammatory infiltrates and fibrosis become more prominent in the persisting disease and may be difficult to distinguish from (coexisting) rejection. Detection of polyomavirus-inclusion bearing cells ('decoy cells') in the urine and quantification of BK virus DNA in the plasma have been proposed as surrogate markers for polyomavirus replication and allograft disease, respectively. Antiviral treatment is not yet established; however, reports of treatment with cidofovir are encouraging. Current management aims at the judicious modification and/or reduction of immunosuppression which, in view of preceding or concurrent rejection, is not without risk.