It was previously reported that the cell membrane expression of HLA class II molecules is tissue specific and variable among individuals. This variation could be explained at the level of gene regulation. Due to the fact that a coordinate regulation of the HLA-DR genes seems to exist, we focused on the HLA-DRA monomorphic gene. In order to study the polymorphism of the HLA-DRA gene regulatory region, we used restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-amplified genomic DNA. The DdeI and PvuII digestions of the amplified DNA permitted the definition of the two alleles according to the absence (allele A) or the presence (allele B) of the two polymorphic restriction sites. The presence of these sites was confirmed by direct sequencing after PCR. Using homozygous typing cells, a close relationship between the HLA-DRB coding region and the HLA-DRA regulatory region polymorphisms was shown. Furthermore, a linkage between the HLA-DRA regulatory region and DRB3 gene coding region polymorphisms could be established. These results suggested a structural argument for different levels of HLA class II genes and, consequently, of cell-surface expression of class II antigens according to the allelic specificities of DRA, DRB1, and DRB3.