APOBEC3G restricts retrovirus replication through inducing guanosine-to-adenosine (G-to-A) hypermutations in viral DNA. Its role in brain "intrinsic immunity" has not been elucidated nor has it been convincingly demonstrated which brain cell compartments produce this defense factor in human immunodeficiency virus (HIV) infection, acquired immunodeficiency syndrome (AIDS), and antiretroviral therapy. Here, we investigated by immunohistochemistry and in situ hybridization the cell-specific regulation of APOBEC3G in rhesus macaque brains during infection with simian immunodeficiency virus (SIV) clone deltaB670, a primate model of HIV disease. We found that APOBEC3G protein and mRNA were exclusively expressed by some perivascular macrophages throughout the brain of noninfected and asymptomatic SIV-infected monkeys. Depending on virus burden, APOBEC3G was induced in microglia/macrophage-derived cells and T lymphocytes in late-stage SIV infection. Intracellularly, APOBEC3G was found in the cytoplasm and/or in the nucleus. APOBEC3G-positive cells were in close proximity to SIV gag-positive cells or were SIV-copositive. Induction of APOBEC3G was accompanied by G-to-A hypermutations in the gag and pol regions of retroviral DNA isolated from brain sections of AIDS-symptomatic monkeys. Although brain-directed treatment with antiretroviral 6-chloro-2',3'-dideoxyguanosine suppressed brain SIV burden, encephalitis and reduced cerebral APOBEC3G synthesis hypermutations were still detectable. Upregulation of APOBEC3G may restrict spread of SIV in the brain and thus limit brain damage during lentiviral infection.