Microglia are the resident macrophages of the brain, and when activated, have functions including cytokine production, phagocytosis and antigen presentation. The class II MHC genes encode proteins that present antigenic peptides to helper T cells, leading to T cell activation and the development of an antigen-specific immune response. Class II MHC gene expression is strictly regulated by the class II transactivator (CIITA) transcription factor. In this study, we investigated the effects of various immunomodulatory cytokines on IFN-γ induction of class II MHC and CIITA gene expression in microglia, both primary microglia and a murine microglial cell line, EOC 20. By flow cytometry analysis we show that IFN-γ-induced surface expression of class II MHC molecules on EOC 20 cells can be inhibited by the cytokines TGF-β1, IL-4 and IL-10, but not IL-13. Using a ribonuclease protection assay, we have found that TGF-β1, IL-4 and IL-10 act by inhibiting the expression of IFN-γ-induced CIITA mRNA and, in turn, class II MHC mRNA. TGF-β1, IL-4, and IL-10 inhibition of IFN-γ-induced CIITA mRNA accumulation was not due to destabilization of CIITA mRNA, suggesting an effect at the level of transcription. In primary murine microglia, IL-10 and TGF-β1 inhibited IFN-γ-induced CIITA and class II MHC expression. However, a discordant effect of IL-4 was noted in that IL-4 enhanced IFN-γ-induced CIITA and class II MHC expression in primary microglia. Although some differences are observed between EOC 20 cells and primary microglia in terms of responsiveness to TGF-β, IL-4 and IL-10, CIITA and class II MHC gene expression are coordinately modulated.