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 (DRI-7) were radiolabeled with [3Htyrosne.a and ( chains were Isolated from CC11.23-reactive preparations, and their amino-terminal tyrosine sequences were determined. Each DR haplotype (with the exception of DRw6) * Although the DR a chain appears to be nonpolymorphic(1), a growing body of evidence suggests that the DQ a chain is polymorphic (8-11). Comparisons of genomic and/or cDNA sequences of DQ a chain from several cell lines have demonstrated that multiple differences exist among the few haplotypes examined (9, 10). Polymorphic variation of both the a and ( chain of the DQ molecule is consistent with the extensive polymorphism exhibited by its murine counterpart, the I-A molecule. Both the a and (8 chains of I-A molecules display variation from one haplotype to another (15). In addition to these extensively polymorphic I-A chains, the mouse expresses a modestly polymorphic I-E a chain and a highly polytnorphic I-E (3 chain. A similar situation appears to exist within the human counterpart ofI-E, the HLA-DR subregion. Existing data are consistent with the notion that the DR a chain is invariant, or at best only modestly variant, but that the DR ( chain, the DQ a chain, and the DQ P chain are polymorphic among different haplotypes.Shortly after the demonstration of allelic polymorphism of murine class II molecules, evidence was presented for the formation of hybrid molecules in F1 animals, providing a possible molecular mechanism for the phenomenon of gene complementation (16,17). This trans gene complementation increases the alloantigen repertoire in heterozygotes. In humans, tranls association has recently been reported for DQ molecules by two-dimensional gel electrophoresis (18