The histological diagnosis of BK or JC polyomavirus allograft nephritis (PVAN) requires evaluation of a renal biopsy with demonstration of the polyomavirus cytopathic changes and confirmation with an ancillary technique such as immunohistochemistry. Three histological patterns of PVAN (A, B, and C) are identified in renal biopsies. Pattern A corresponds to the early disease, whereas patterns B and C identify intermediate and very advanced histological changes, respectively. The histological pattern found in the first biopsy correlates with graft outcome. Because PVAN affects the kidney in a random, multifocal manner, a negative biopsy does not rule out the disease. Patients with BK PVAN characteristically have high levels of BK viruria and viremia. Although the cutoff values of viral loads have not been fully determined, there is general agreement that BK viruria of >10(7)/mL and BK viremia of >10(4) are typical of patients with a biopsy showing BK PVAN. Prospective evaluation of viruria with urine cytology (decoy cells) and/or quantitative polymerase chain reaction can aid in the identification of patients at risk for developing PVAN. In addition to histological evaluation, viremia has emerged as the most specific test for the diagnosis of BK PVAN. JC PVAN is very infrequent in comparison with BK PVAN, but is also characterized by large viruria (>10(4)). On the other hand, JC viremia appears to be lower, in the order of 10(3)/mL. The inflammatory changes in PVAN need further characterization. Currently, there are no tools to differentiate acute cellular rejection from viral specific T-cell response.