Polyomavirus infection commonly occurs in childhood and adolescence, remaining in a latent status and reactivated in an immunocompromised status. We report herein an autopsy case of HIV-positive 41-year-old male, who succumbed to disseminated Kaposi sarcoma and cytomegalovirus infection involving the gastrointestinal tract, lung and brain. The involved kidney showed minimal inflammatory infiltrates and tubular injury: the nuclei of tubular epithelial cells were markedly enlarged with central clearing and peripheral chromatin margination or bore basophilic nuclear inclusions. Inclusion-bearing tubular epithelial cells were negative for the viral immunostains including herpes simplex virus, Epstein-Barr virus and adenovirus. Electron microscopy disclosed 42 nm intranuclear viral particles compatible with the BK polyomavirus. The viral particles were icosahedral in paracrystalline array and nonenveloped.