Hepatitis C virus (HCV) is a leading cause of liver damage and has also been implicated in extrahepatic pathologies. We examined for HCV RNA paired CSF and plasma samples from 12 viremia positive patients using PCR. The CSF from 5/5 HIV-infected patients and 5/7 HIV-negative patients were HCV RNA positive. Branched DNA analysis showed that HCV loads in CSF were much lower than in plasma. Several HCV-positive CSF showed no evidence of blood contamination, impaired blood-brain barrier, or intrathecal IgG production. Comparison of HCV quasispecies in three sets of samples suggested that the virus in CSF was of plasma origin.