Hepatitis C virus (HCV) infection often is associated with cognitive dysfunction and depression. HCV sequences and replicative forms were detected in autopsy brain tissue and cerebrospinal fluid from infected patients, suggesting direct neuroinvasion. However, the phenotype of cells harboring HCV in brain remains unclear. We studied autopsy brain tissue from 12 HCV-infected patients, 6 of whom were coinfected with human immunodeficiency virus. Cryostat sections of frontal cortex and subcortical white matter were stained with monoclonal antibodies specific for microglia/macrophages (CD68), oligodendrocytes (2,3-cyclic nucleotide 3-phosphodiesterase), astrocytes (glial fibrillary acidic protein [GFAP]), and neurons (neuronal-specific nuclear protein); separated by laser capture microscopy (LCM); and tested for the presence of positive-and negative-strand HCV RNA. Sections also were stained with antibodies to viral nonstructural protein 3 (NS3), separated by LCM, and phenotyped by real-time PCR. Finally, sections were double stained with antibodies specific for the cell phenotype and HCV NS3. HCV RNA was detected in CD68-positive cells in eight patients, and negative-strand HCV RNA, which is a viral replicative form, was found in three of these patients. HCV RNA also was found in astrocytes from three patients, but negative-strand RNA was not detected in these cells. In double immunostaining, 83 to 95% of cells positive for HCV NS3 also were CD68 positive, while 4 to 29% were GFAP positive. NS3-positive cells were negative for neuron and oligodendrocyte phenotypic markers. In conclusion, HCV infects brain microglia/macrophages and, to a lesser extent, astrocytes. Our findings could explain the biological basis of neurocognitive abnormalities in HCV infection.Patients with chronic hepatitis C virus (HCV) infection were reported to be more likely to manifest impairments in the quality of life, fatigue, and depression than patients with liver disease of other etiology (3,12,14,39). More recently, HCV infection was associated with cognitive dysfunction (11, 13). Importantly, Forton and colleagues, using proton magnetic resonance spectroscopy ( 1 H MRS), demonstrated elevations of choline/creatine ratios in basal ganglia and white matter in patients with mild hepatitis C disease that were not present in healthy volunteers or patients with hepatitis (9, 11). The presence of similar abnormalities consisting of increased choline and reduced N-acetyl aspartate levels among HCV-positive patients relative to those of controls has since been reported by other researchers (25, 41). The 1 H MRS changes in HCV infection are different from those seen in hepatic encephalopathy, where the choline ratios are depressed (40), but are similar to those found in patients with human immunodeficiency virus (HIV) infection (24, 26). Additional evidence for the biological basis of HCV-related cognitive dysfunction is provided by a recent report showing differences in gene expression patterns between brain tissue from HCV-positive and HCV-nega...