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Recently, we found that some parenchymal microglia in brain of HIV<jats:sup>+<\/jats:sup> subjects without encephalitis (HIV\/noE) but with varying degrees of neurocognitive impairment express CD16 and CD163, even in the absence of detectable virus production. To further our understanding of microglial activation in HIV, we investigated expression of specific genes by profiling parenchymal microglia from archival brain tissue of patients with HIVE and HIV\/noE, and HIV<jats:sup>\u2212<\/jats:sup> controls.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Single\u2010population microarray analyses were performed on \u223c2,500 laser capture microdissected CD163<jats:sup>+<\/jats:sup>, CD16<jats:sup>+<\/jats:sup>, or CD68<jats:sup>+<\/jats:sup> M\u03a6s\/microglia per case, using terminal continuation RNA amplification and a custom\u2010designed array platform.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Several classes of microglial transcripts in HIVE and HIV\/noE were altered, relative to HIV<jats:sup>\u2212<\/jats:sup> subjects, including factors related to cell stress, immune activation, and apoptosis. Additionally, several neurotrophic factors were reduced in HIV infection, suggesting an additional mechanism of neuropathogenesis. The majority of transcripts altered in HIVE displayed intermediate changes in HIV\/noE.<\/jats:p><\/jats:sec><jats:sec><jats:title>Interpretation<\/jats:title><jats:p>Our results support the notion that microglia contribute to the maintenance of brain homeostasis and their potential loss of function in the context of chronic inflammation contributes to neuropathogenesis. Furthermore, they indicate the utility of profiling M\u03a6s\/microglia to increase our understanding of microglia function, as well as to ascertain alterations in specific pathways, genes, and potentially, encoded proteins that may be amenable to targeted treatment modalities in diseases affecting the brain. 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