We have investigated the origin of intraepithelial lymphocytes (IEL) populations in the murine gut, using reconstitution experiments in which the presence of thymus-derived cells of host or donor origin is rigorously controlled: RAG(-/-) mutant mice which have no T cells, were injected either with the bone marrow (BM) cells of nude mice or with selected peripheral lymph node (LN) T cells of euthymic mice. In thymectomized RAG(-/-) mice, injection of BM cells from nude mice led, after 2 mo, to the development of a peripheral B cell compartment and to the appearance, in the gut, of IEL bearing homodimeric CD8 alpha chains and either gamma/delta or alpha/beta TCR. In RAG(-/-) mice with a thymus, a similar injection led to complete lymphoid reconstitution, with the additional appearance in the gut of CD4(+), CD8 alpha/beta(+) or CD4(+)CD8 alpha/alpha(+) IEL, all bearing alpha/beta TCR. In contrast, injection of LN T cells into these mice reconstituted a gut IEL population made of CD4(+), CD8 alpha/beta(+), or CD4(+) CD8 alpha/alpha(+) cells, all bearing alpha/beta TCR; CD8 alpha/alpha(+) TCR-gamma/delta(+) or alpha/beta(+) IEL were not observed. These results demonstrate that the thymus and/or thymic-derived peripheral T cells are absolutely required for the generation of CD4(+), CD8 alpha/beta(+), and CD4(+)CD8 alpha/alpha(+) IEL, which are thus thymus dependent. In contrast, TCR(+) CD8 alpha/alpha(+) IEL appear in the absence of the thymus, and thus are thymus independent.