Transcription of major histocompatibility complex (MHC) class II genes is controlled primarily by the promoter, which contains several conserved cis-acting elements, including the X, X2, and Y boxes. We show here that RFX, the X box-binding protein that is deficient in certain MHC class II regulatory mutants, binds cooperatively with an X2 box-binding protein (X2bp) to form an RFX.X2bp.DNA complex in which the interaction of the two factors with their target sites is strongly stabilized. A functional role of this RFX.X2bp complex is consistent with mutational analysis of the X and X2 boxes of the DRA and DRB1 class II promoters. Together with previous results demonstrating cooperative binding between RFX and the Y box-binding protein NF-Y, our results indicate that RFX plays a central role in promoting cooperative binding interactions required for stable occupation of the MHC class II promoter. This may explain why the highly specific defect in binding of RFX observed in certain MHC class II regulatory mutants is associated in vivo with a bare promoter in which all of the cis-acting elements, including the X, X2, and Y boxes, are unoccupied.