Previous studies have shown that two CCAAT/enhancer binding protein (C/EBP) binding sites (sites I and II) within the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) are critically important for efficient virus replication within cells of the monocyte lineage, a primary cell type infected by HIV-1. Sequence variation at C/EBP sites I and II has been shown to alter the affinity of C/EBP factors to these sites. Specifically, sequence variation within C/EBP binding site II has been shown to alter binding of purified C/EBP beta protein and basal activity of the HIV-1 LTR. We have previously demonstrated that the C/EBP site II consensus cladeB (ConB) variant was highly conserved in brain- and peripheral blood-derived LTRs of individuals with advanced HIV-1 disease. Given these important observations, the regional distribution of LTRs containing the C/EBP site II ConB variant derived from brain tissues of patients with and without HIV-1-associated dementia (HIVD) was examined. A statistically significant difference was found in the distribution of LTRs containing the C/EBP site II ConB variant in brain regions derived from patients with and without HIVD. In addition, we have previously shown that LTRs containing C/EBP site II 4C and 6G variants (designated according to the position at which nucleotide change occurred relative to ConB, followed by the actual nucleotide found at the variant position) were only found in brain tissue of patients with HIVD. As an extension of these observations, the regional distribution of LTRs containing C/EBP site II 4C or 6G variants derived from the brains of patients with HIVD was examined and a statistically significant difference was observed. We have shown that LTRs containing a low-affinity C/EBP site II 4C variant accumulated in the cerebellum. LTRs containing the 4C site variant in conjunction with the consensus cladeB (ConB) site I exhibited the lowest basal LTR activity of any of the LTRs examined. These results suggest that LTRs containing the C/EBP site II 4C configuration may promote the establishment of a latent provirus in the cerebellum, a region of the HIVD brain that exhibits little viral gene expression. Furthermore, LTRs containing a high affinity C/EBP site II 6G variant accumulated in the mid-frontal gyrus, a site of highly productive replication. In addition, LTRs containing the C/EBP site II 6G variant with the ConB at site I exhibited the highest basal LTR activity. In conclusion, distinct LTR populations with specific C/EBP site II configurations were found in different neuroanatomical regions of the brain, potentially due to differences in the molecular architecture of the LTR, viral entry pathways, and/or brain microenvironments.