Class II-deficient combined immunodeficiency (CID) is a hereditary disease resulting in abrogation of transcription of the class II genes of the major histocompatibility complex, due to a defect in a trans-acting regulatory factor. Cell lines from certain CID patients lack factor binding at multiple sites in class II promoters in vivo. A mutation in one of the promoter binding proteins could explain this 'bare' phenotype only if these factors bind cooperatively or in a temporal hierarchy. Alternatively, the mutation could affect the configuration of the promoter within the MHC locus. Here, we provide evidence that the factor(s) defective in class II-deficient CID controls the accessibility of class II promoters within the environment of the MHC. The in vivo occupancy of wild type and mutated class II promoter constructs was examined in stable transfectants of normal and CID-derived cell lines. The CID promoter phenotype could not be reproduced in a normal cell line by eliminating binding at any one promoter element, suggesting that these factors bind independently, both spatially and temporally. In contrast, promoter occupancy was partially restored in two CID lines at a randomly integrated wild type promoter, implying that the promoter is inaccessible to factors in its native environment, but accessible when moved to another location in the genome.