Objective: The objective is to establish the presence of JC and/or BK polyomavirus in HIV patients with symptoms of encephalitis and/or meningitis.Methodology: From September 2009 to December 2011, a prospective study was conducted.34 HIV patients with symptoms consistent with encephalitis and/or meningitis were included.The work was conducted in 3 hospitals in the city of Monteria.Viral DNA extraction was performed on samples of cerebrospinal fluid (CSF) using a commercial kit (Quiagen, USA).The detection of BKV and JCV was performed by multiplex realtime PCR (LightMix®, Roche Diagnostics, Germany) with primers specific for the short t antigen gene fragment, labeled probes and one internal control.Results: In 9 (26%) of 34 patients included in the study, JCV virus was detected; only 1 (3%) patient had coinfection with JCV/BKV.The mortality rate was 3%.The cytochemical examination of CSF in positive patients presented average values: 40.7 mg/dL glucose, 171.66 mg/dL protein, 19.8 mm 3 leukocytes, and 109.8 mm 3 erythrocytes.Conclusion: The findings demonstrate that JCV and BKV have a significant occurrence in HIV patients with CSF infections in Monteria.