Up to 10% of renal transplant recipients can develop polyomavirus nephropathy (PVN) in the allograft, leading to premature graft failure. Recent studies have shown that early diagnosis of PVN before there is irreversible damage to the kidney can result in marked improvement of outcome with resolution of the infection in a large proportion of patients. Early histopathologic diagnosis is complicated by the subtle beginning of the infection and its multifocal nature. This review presents a comprehensive set of guidelines for the effective clinical use of urine cytology and quantitation of viruria and viremia in conjunction with the renal biopsy findings. The morphological features of PVN are presented with specific emphasis on the patterns of PVN that are based on the histological progression of the disease and that correlate with clinical outcome. Also discussed in the context of their clinical significance are the main virological and epidemiological aspects of the BK, JC, and SV40 polyomavirus infections.