Polyomaviruses may cause human disease, particularly in immunocompromised hosts. JCV, one of the members of polyomaviridae family, is the causative agent of the neurological disease progressive multifocal leukoencephalopathy (PML), which occurs mostly in immunocompromised patients. Progressive Multifocal leukoencephalopathy (PML) is a progressive demyelinating disorder of the central nervous system (CNS) resulting from infection of oligodendrocytes by JC polyomavirus. Whereas after highly active antiretroviral therapy (HAART), the incidence of nearly all of all neurological complication have decreased, this article evaluates the incidence and prognosis of JC polyomavirus-associated PML including a unchangeable incidence of PML associated with JC polyomavirus compared with other opportunistic disease and paradoxical results of disease remission in HAART era.