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Combination antiretroviral (ARV) therapy can reduce human immunodeficiency virus (HIV) RNA levels in cerebrospinal fluid (CSF) and plasma and improve immunocompetence. However, HIV-associated neurocognitive disorders persist, possibly because some ARV drugs do not reach therapeutic concentrations in the brain. The primary objective of this study was to determine whether lopinavir plus ritonavir (LPV-rtv) used alone reduced the HIV RNA level in CSF.The study was an open-label, 24-week trial of sequential ARV therapy. Fifteen subjects were enrolled and received LPV-rtv therapy. Ten subjects reached the primary study end point at week 3, before at least 2 other ARV drugs were added to the treatment regimen. CSF and blood samples were obtained before treatment and after 3, 12, and 24 weeks of treatment.LPV-rtv therapy alone reduced the HIV RNA level in CSF in all subjects (median change in HIV RNA level, -1.42 log10 copies/mL), including 5 who had slower decreases in HIV RNA level in CSF than in plasma—an indicator of autonomous central nervous system infection. Among 9 subjects who completed 12 weeks of LPV-rtv—containing therapy, the HIV RNA level was below quantitation in the CSF samples from 8 subjects and in the plasma samples from 6 subjects. By week 24, HIV RNA levels were below quantitation in samples of both fluids from all 8 subjects.LPV-rtv therapy alone for 3 weeks consistently reduces the HIV RNA level in CSF by at least 10-fold in most individuals, including those likely to have autonomous HIV replication in the central nervous system. Because it penetrates the central nervous system in therapeutic concentrations and appears to reduce HIV replication in the central nervous system, LPV-rtv may benefit subjects who receive a diagnosis of or are at risk for HIV-associated neurocognitive disorders.