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Autoantigen-specific encephalitogenic T cells gaining access to the central nervous system (CNS) and leading to self-destructive inflammation are the critical driving force for multiple sclerosis (MS). It has been shown that peripherally primed T cells have to infiltrate into the CNS and to get reactivated by antigen-presenting cells (APCs) in order to induce inflammation in experimental autoimmune encephalomyelitis (EAE), an animal model of MS. The contributions of macrophages and dendritic cells as APCs at the border between CNS and periphery were shown. However, antigen presentation in CNS remains largely undefined; especially the function of glia cells as APCs remains elusive. Microglia are the only CNS-resident immune cells, thus their potential function in regulating T cell activation cannot be overlooked. In this study, we determined to understand the relationship between microglia and T cells. Live imaging revealed that naive microglia or LPS-stimulated microglia cannot induce the activation of NFAT-GFP-expressing MBP-specific T cells (TMBP-NFAT-GFP cells) and NFAT-GFP-expressing OVA-specific T cells (TOVA-NFAT-GFP cells), indicated by translocation of NFAT-GFP from cytosol into the nucleus. Interestingly, Interferon-�� (IFN-��)-stimulated microglia significantly induced activation of both TMBP-NFAT-GFP cells and TOVA-NFAT-GFP cells even without the presence of cognate antigen, indicating antigen-independent T cell activation by microglia, which are regulated by IFN-��. In addition, by comparing macrophages and microglia in the CNS of rats with EAE, we showed that macrophages were more efficient APCs than microglia. Interestingly, IFN-��-stimulated microglia and microglia from EAE rats showed similar T cell stimulation capacity. IFN-��, a signature cytokine of TH1 cells, was highly upregulated in both TMBP cells and TOVA cells after co-culturing with naive microglia even without the presence of cognate antigens, suggesting microglia regulate T cell activation antigen-independently. Furthermore, we evaluated different cytokine expression in TMBP cells and TOVA cells after co-culturing with microglia and found two innate cytokines, tumor necrosis factor �� (TNF-��) and interleukin-1�� (IL-1��), were highly upregulated. The induction of these cytokines required direct contact of T cells and microglia. Intriguingly, knockout TNF-�� in T cells by using CRISPR/Cas gene editing showed that TNF signaling regulated IL-1�� production. Moreover, IL-2R, OX-40 and major histocompatibility complex class II (MHCII) were highly upregulated on both TMBP cells and TOVA cells after co-culturing with microglia in absence of antigen, which further support the idea that microglia regulate T cell activation antigen-independently. Beside of microglia, we looked at whether astrocytes activate T cells as similar as microglia. However, astrocytes were not as strong as microglia in inducing T cell activation. To characterize the transcriptome profile of microglia and macrophages at the early stage of EAE, we performed RNA-sequencing analysis. Compared to naive microglia, microglia from EAE rats showed strong enrichment of genes associated with IFN-�� signaling, suggesting that microglia are influenced by TH1 cells. Moreover, microglia strongly upregulated chemokines such as Cxcl9, Cxcl10, Cxcl11 and Ccl5 which are important for T cell recruitment into the CNS. Although macrophages have a higher T cell stimulating capacity than microglia, at the very early stage of EAE, microglia are the main myeloid cells in the CNS that activate T cells before macrophages penetrate into the CNS. In summary, our study showed that in addition to antigen-dependent manner, microglia can regulate T cell differentiation and activation antigen-independently. Although macrophages showed higher T cell activating capacity, their number is low at early stages of EAE. At that time point, microglia can stimulate T cells and induce production of inflammatory cytokines. In addition, as results of interaction with T cells, microglia produced chemokines, which could be important for the further recruitment of T cells and macrophages.