Of 41 wild-derived mouse strains analyzed, 14 contained T cells bearing V beta 17 receptors in spite of the concomitant expression of I-E antigens. Reciprocal F1 and F2 hybrids of one of these strains, PWK, with laboratory strains revealed different patterns of V beta 17 T cell deletions from those observed with V beta 17 T cells from SJL, implying that the two V beta 17 regions are associated with recognition of distinct superantigens. The structures of the V beta 17 alleles differ by two amino acid substitutions, which lie together in an area distant from the predicted site of T cell receptor interaction with peptide-MHC complexes but overlapping with that implicated in V beta 8.2 recognition of Mls-1 superantigen. This demonstrates that the self-superantigen leading to V beta 17 T cell deletion varies with the allele of the receptor gene and confirms that T cell deletions by such ligands involve interactions with a region of the V beta domain that is distinct from the conventional combining site.