We have studied V alpha 2 and J beta usage by V beta 6+CD4+ peripheral T cells isolated from the congenic mice strains BALB/c (Mls-1b) and BALB.D2 (Mls-1a). We found that the TCR beta-chain of V beta 6+CD4+ T cells present in adult Mls-1a mice differed from those in Mls-1b mice; the fraction of V beta 6+CD4+T cells using the J beta 2.7 segment was reduced, while the number of V beta 6+CD4+ T cells using J beta 1.2 was augmented. These results indicate that the CDR3 region of the TCR beta-chain participates in recognition of the Mls superantigen. We also found that in Mls-1a mice an increased fraction of V beta 6+CD4+ T cells expressed the V alpha 2 chain. The study of J beta usage by V beta 6+CD4+V alpha 2+ and V beta 6+CD4+V alpha 2- T cells indicates that both J beta segment and TCR V alpha 2 chain expression confer complementary protection against deletion by Mls-1a superantigen. These results suggest a novel view of Mls-1a-driven selection, where the CDR3 region of the V beta chain modulates superantigen recognition, and the affinity/avidity of the TCR-MHC-superantigen complex determine the fate of the T cell.