Factors dependent on the host, the virus, and the allograft affect the course of polyomavirus allograft nephropathy (PVAN). Development of specific cytotoxic antiviral immunity requires recognition of host human leukocyte antigen (HLA) molecules together with viral peptides on the target cells. We correlated the number of matched HLA-A, HLA-B, and HLA-DR antigens with graft outcome in 90 patients with PVAN. Patients that maintained graft function had significantly less degrees of HLA matching (mean 1.5) in comparison to patients with graft loss (mean 2.87, P= 0.001). Markedly reduced incidence of graft loss was observed in patients with no HLA matching whatsoever in comparison to patients with any degree of matching (P= 0.003). Lack of HLA matching may impair the host's ability to mount an effective antiviral cytotoxic immune response. An adequately developed antiviral cellular immunity may lead to significant tissue damage and graft loss even if the viral infection is eventually controlled.