A monoclonal antibody, CC11.23, with monomorphic specificity predominantly for products of the HLA-DQ subregion, has been used to demonstrate primary structural variation among DQ molecules. Two cell lines of each haplotype (DR1-7) were radiolabeled with [3H]tyrosine. alpha and beta chains were isolated from CC11.23-reactive preparations, and their amino-terminal tyrosine sequences were determined. Each DR haplotype (with the exception of DRw6) was found to express a distinct DQ molecule with a minimum of three allelic forms of the DQ alpha chain and five allelic forms of the DQ beta chain. At the primary structural level, the locus for the DQ beta chain appears to be as polymorphic as the locus for the DR beta chain. Unlike the locus for the DR alpha chain (which is essentially nonpolymorphic), the locus for the DQ alpha chain was found to be polymorphic. Comparison of DQ molecules from two different heterozygous cell lines with those from homozygous cell lines revealed that in heterozygotes, DQ alpha chains from either allele can associate with DQ beta chains from one allele. The formation of hybrid HLA-DQ molecules by both cis and trans gene complementation, coupled with several polymorphic forms of each of the DQ subunits, considerably increases the repertoire of DQ alloantigens in heterozygotes.