Polyoma nephropathy is an increasingly prevalent complication in kidney transplant recipients. We identified tubular basement membrane immune complexes in allograft recipients with polyoma nephropathy. To evaluate this lesion, biopsies demonstrating polyoma infection over a 2-year period were assessed for the presence, localization, and composition of tubular basement membrane immune complexes including simian virus 40 (SV40) antigen and for histologic classification according to Drachenberg. Charts were reviewed for clinical information. Thirteen of 26 biopsies from 11 of 20 patients demonstrated tubular basement membrane immune complexes, all of which contained C3, immunoglobulin G, and SV40 antigen. Deposits were in all nephron segments associated with tubular cell viral infection and tubulointerstitial inflammation; no SV40 antigen was in glomeruli. The Drachenberg histologic classification tended to be more advanced in biopsies with tubular basement membrane immune complexes, but not significantly so. There were no differences in patients with and without immune complexes with respect to age, sex, time after engraftment, and plasma viral load. Tubular basement membrane immune complexes were present in 5 of 6 patients who lost renal function and in 5 of 12 with currently functioning grafts (P < .1). Polyoma-associated tubular basement membrane immune complexes seem to be a local phenomenon, likely related to viral antigen shedding. The clinical significance is uncertain but may portend a worse prognosis.