The four V beta gene segments, V beta 1, 3.1, 6, and 10, which previously have been shown by RFLP analyses to differ between TCR V beta a and V beta b haplotypes, were cloned and sequenced from V beta a SWR mice and compared with V beta b strains to define coding sequence polymorphisms distinguishing these haplotypes. V beta 3.1 and 6 alleles differed between strains by a single amino acid, whereas V beta 1 and 10 alleles differed by 4 and 6 amino acids, respectively. The overall interhaplotypic V beta polymorphisms appeared to be limited when based upon compilation of this information and previously published V beta sequences. One application of these data was to attempt to elucidate the molecular basis underlying the recently reported allele-specific autoimmune disease, collagen-induced arthritis. Based on the present structural data and the additional evidence, contrary to what was suggested, the V beta 6 gene does not appear to be the sole participant in anticollagen responses.