Monocytes/macrophages are critical components of HIV and SIV encephalitic lesions. We used in vivo BrdU labeling and markers specific to stages of macrophage differentiation or inflammation to define macrophage heterogeneity and to better define the role of macrophage populations in lesion formation and productive infection. Lesions were heterogeneously composed of resident macrophages (CD68⁺HAM56⁺), perivascular macrophages (CD163⁺ CD68⁺MAC387⁻), and recently infiltrated MAC387⁺ CD68⁻CD163⁻ monocytes/macrophages. At 24 and 48 hours after BrdU inoculation, 30% of MAC387⁺ monocytes/macrophages were BrdU⁺, consistent with their being recently infiltrated. In perivascular cuffs with low-level SIV replication, MAC387⁺ monocytes/macrophages outnumbered CD68⁺ macrophages. Conversely, lesions with numerous SIV-p28⁺ macrophages and multinucleated giant cells had fewer MAC387⁺ monocytes/macrophages. The MAC387⁺ cells were not productively infected nor did they express detectable CCR2, unlike perivascular macrophages. Overall, we found that the proportion of MAC387⁺ cells tends to be higher than the proportion of CD68⁺ macrophages in the brain of animals with mild encephalitis; the ratio was reversed with more severe encephalitis. These results suggest that development of SIV and HIV encephalitis is an active and ongoing process that involves the recruitment and accumulation of: i) nonproductively infected MAC387⁺ monocytes/macrophages that are present with inflammation (potentially M1-like macrophages), ii) CD163⁺ perivascular macrophages (consistent with M2-like macrophages), and iii) CD68⁺ or HAM56⁺ resident macrophages. The latter two populations are cellular reservoirs for productive infection.