We demonstrate that in the mouse intestinal epithelium the selection of T lymphocytes expressing a transgenic T cell receptor alpha/beta (TCR-alpha/beta) specific for male antigen (H-Y) in the context of H-2D(b) depends on the differential expression of H-Y and H-2D(b) in situ. In H-2D(b) transgenic males, there is no reduction in the number of intestinal intraepithelial lymphocytes (IEL), and the four main subsets of IEL expressing TCR-alpha/beta, defined by the differential expression of CD4, CD8alpha, and CD8beta, are present. Moreover, the level of expression of CD8alpha and CD8beta on CD8+ IEL subsets is unaltered. The frequency of CD8alpha+ IEL expressing CD8beta, in H-2D(b) male mice, however, is significantly decreased and these cells do not express the transgenic TCR. In contrast, virtually all CD8alpha+beta- IEL in the same animals express the transgenic TCR. Still, these potentially autoreactive cells are refractile to H-Y/H-2D(b) stimulation in vitro. Both H-2D(b) and H-2D(d) transgenic females contain high frequencies of cells expressing the transgenic TCR among CD8alpha+beta- and CD8alpha+beta+ IEL. However, two possibly related phenotypic features are peculiar to H-2D(b) female mice. The frequency of CD8alpha+beta+ IEL expressing CD8beta is increased in these mice and, while in H-2D(d) females the level of the transgenic TCR alpha chain expressed on CD8alpha+beta+ IEL is uniformly low, some of the CD8alpha+beta+ IEL in H-2D(b) females express a high level of both transgenic TCR chains. It is important to note, the ability of CD8alpha+beta+ IEL to respond to H-Y/H-2D(b) stimulation in vitro is restricted to those coexpressing a high level of both transgenic TCR chains. The analysis of athymic radiation chimeras using adult thymectomized recipients of distinct H-Y/H-2 haplotypes, reconstituted with bone marrow from H-2D(b) transgenic females, demonstrates that all IEL subsets present in unmanipulated transgenic animals develop in the absence of a thymus. These IEL are phenotypically identical to those found in unmanipulated transgenic animals sharing the H-Y/H-2 haplotype of athymic recipients. Taken together, these results demonstrate that in the absence of male antigen, expression of H-2D(b) in the intestinal epithelium results in the positive selection of functional IEL specific for male antigen, in situ. When both H-Y and H-2D(b) are expressed in the intestinal epithelium, CD8alpha+beta+ IEL expressing the transgenic TCR are negatively selected, while the frequency of nonfunctional CD8alpha+beta- IEL expressing the transgenic TCR is increased. Thus, while the functional T cell repertoire generated in the thymus and in the intestinal epithelium of these transgenic animals is similar, the supporting mechanisms are distinct.