A special class of self-antigens (endogenous superantigens) is capable of deleting many murine T cells on the basis of their expression of particular T-cell receptor V beta gene segments. In mice that endogenously express these antigens, tolerance is mediated in part by the clonal deletion of the relevant V beta-bearing T cells. The deletion of I-E-reactive V beta 5.2-bearing T cells is dependent on the coexpression of an I-E tolerogenic coligand (Etc)14 and the gene for one of these coligands, Etc-1, maps to chromosome 12, near the mouse mammary tumour viral integrant, Mtv-9. Here we report a perfect genetic linkage between Etc-1 and Mtv-9 and show that Etc-1 is also involved in the I-E-dependent deletion of T cells bearing V beta 5.1 and V beta 11 domains. We also demonstrate that Mtv-9 transcripts are present in B cells expressing Etc-1 and suggest that the coligand recognized by roughly 15% of all T lymphocytes is encoded by the Mtv-9 genome.