The monoclonal antibodies Genox 3.53, S1, and R1 define polymorphic epitopes localized to DQ molecules. All three antibodies showed a strong association with the HLA-DR antigens 1, 2, and w6 when tested on a panel of 68 unrelated individuals, suggesting that they all recognized the DQw1 allospecificity. However, segregation analysis and binding studies with a panel of HLA-D/DR homozygous cells indicated that these monoclonal antibodies defined two different alloantigens. Cells homozygous for DR 1, 2, or w6 expressed the epitopes defined by all three antibodies (i.e., S1, R1, and Ge) while cells homozygous for DR4 and DRw8 expressed only the S1 and R1 epitopes. Sequential immunoprecipitation analyses in S1+/R1+/Ge+ individuals, in which the three epitopes were shown by segregation analysis to be encoded by the same chromosome, revealed two distinct DQ-like molecules. While R1 and S1 appeared to reside on the same molecule, the epitope defined by Genox 3.53 was on a different molecule. Identical results were obtained with DR1-, DR2-, or DRw6-bearing cells. Thus it appears that DQw1-bearing individuals express two cis-encoded DQ-like molecules that carry distinct alloantigenic specificities.