Viral-induced allograft dysfunction is a significant cause of morbidity and mortality in renal allograft recipients. BK polyomavirus nephropathy continues to be the most common viral disease in renal allografts, although other viruses such as cytomegalovirus (CMV) and adenovirus can have devastating impact on graft function. Proper identification of viral pathogens and distinction from other types of nephritis can be challenging, particularly when the viral infection is at an early stage or when viral inclusions are not frequent. BK polyomavirus nephropathy has occasionally been reported in patients with coexisting CMV infection of other sites or with coinfection documented by serological examination. However, the finding of dual viral infection within a single renal allograft biopsy is unusual. Identification of 1 type of virus within the renal allograft does not preclude the possibility of a second pathological process. This review addresses the key pathological features of BK and CMV nephritis, which should prompt the pathologist to order confirmatory studies to distinguish viral infection from cellular rejection or other forms of allograft nephritis.