We have found cell surface expression of an E alpha molecule in recombinant and transgenic mouse strains lacking an E beta molecule. Flow cytometry has shown low level expression of E alpha in B10.RQB3 (I-AqEk alpha) and B10.RFB2 (I-AfEk alpha) mice. We have also found that B10.Q (H-2q) mice can express the Ek alpha transgene. Since these strains do not have functional E beta chains, we propose that the E alpha A beta hybrid dimers are formed in low numbers and can be picked up by FACS analysis. So far we have not been able to identify these hybrid molecules by cytotoxicity or immunoprecipitation. The E alpha/A beta molecule can function in vivo during thymic selection in the clonal deletion of two V beta TCR subsets, V beta 11 and V beta 6, which have been shown to interact with the intact I-E molecule.