Three cDNA clones encoding a DQ beta and two DR beta polypeptides have been isolated and sequenced from an American black individual expressing a DR2,DQw1 haplotype. The sequences of the cDNA clones are identical to previously described DR and DQ sequences from a DR2,Dw2 cell. The differences between DQw1-associated beta chains from DR2 and DR1 haplotypes is substantial, although a DQw1-specific sequence can be identified. The identical DQ and DR beta sequences found in unrelated individuals from different racial backgrounds suggests that class II structural polymorphism within the human population will be limited.