JCV is associated with Progressive Multifocal Leukoencephalopathy (PML), a fatal demyelinating disease of the central nervous system which occurs majorly in patients with marked cellular immunodeficiency such as HIV/AIDS patients. Sub-Saharan Africa, including Nigeria, has the highest prevalence of HIV as well as HIV co-morbidities globally. Despite this, there is scanty information on the prevalence of JCV infection in Nigeria, especially among immunocompromised persons such as HIV infected individuals in the country. This study was therefore designed to determine the prevalence of JCV among ART naïve HIV infected individuals attending the ART clinic of the University College Hospital (UCH), Ibadan, Nigeria. Two hundred and forty plasma samples consisting of 160 ART naïve HIV positive patients and 80 HIV negative individuals were tested for the presence of JCV by polymerase chain reaction and absolute CD4 count determined using flow-cytometer (Partec, Germany). Clinical and demographic data were also collected from each person after obtaining their informed consent. Thirty-five (35) of the 160 (21.9%) ART naïve HIV infected individuals were positive for JCV DNA while only 5 (6.3%) of the 80 HIV negative individuals tested positive for JCV DNA. The rate of JCV infection was higher among males in both groups. Furthermore, it was observed that a high proportion of ART naïve HIV infected individuals with CD4+ T cell count >500cells/µl at baseline that were infected with JCV cleared the infection six months post ART. Findings from this study show that JCV infection is common among HIV infected individuals.