Although many articles have been published on polyomavirus-induced pathologies in transplant recipients, our knowledge regarding their clinical aspects remains relatively limited. In fact, the number of questions and controversies on the subject seems even to be increasing as new publications continue to appear. This article presents some of these controversies through a brief review of recent clinical facts about the three polyomaviruses that infect humans--JC virus, simian virus 40, and BK virus--as they relate to renal transplantation.