In this study, we addressed B7.1, B7.2, and MHC class II expression on microglia of normal adult C57BL/6J mice, which are susceptible to MOG35-55 peptide-induced experimental autoimmune encephalomyelitis (EAE). We showed that there are two distinct major populations of CD11b(+) cells in the central nervous system (CNS) of naïve mice: CD45 low (CD45(lo); parenchymal microglia) and CD45 intermediate (CD45(int); CNS-associated macrophages). These two populations compose CNS microglia. There is a rare CD45 high (CD45(hi)) population. By contrast, splenic CD11b(+) cells (macrophages) are CD45(int) and CD45(hi), but rarely CD45(lo). CD45(lo)CD11b(+) cells constitutively express much higher levels of B7.1, B7.2, and MHC class II compared to CD45(int) CD11b(+) cells. A shift of CD11b(+) cells from CD45(lo) to CD45(int) was observed in the CNS of EAE mice. Our study provides evidence that (1) CD45(lo) and CD45(hi), but not CD45(int), could be unique markers to differentiate parenchymal microglia from infiltrating macrophages in EAE; (2) the level of CD45 expression on parenchymal microglia (CD45(lo)) was upregulated in EAE; and (3) parenchymal microglia in normal CNS could be potent APCs by expressing high levels of B7.1, B7.2, and MHC class II molecules and could therefore play an important role in inflammation and autoimmunity in the CNS.