To examine the origin of intestinal mucosal T cells and, in particular, unconventional CD8 alpha alpha(+) T cells, we have undertaken a thorough analysis of the gut immune compartment in euthymic and athymic mice carrying either wild-type or mutant transcription factor retinoic acid-related orphan receptor-gamma t (ROR gamma t). We identified a previously unrealized complexity of gut cryptopatch (CP) cells that challenges the previous assertion that CP cells comprise ROR gamma t-expressing adult counterparts of fetal lymphoid tissue inducer (Lti) cells. We showed that many CP cells express intermediate T cell differentiation markers, whether or not they express ROR gamma t, and found that CPs are not completely dependent on ROR gamma t, as previously reported, but merely fewer in number in the ROR gamma t-deficient condition. Indeed, c-kit(+)IL-7R(+)Lin(-)ROR gamma t(-) cells inside the CP and c-kit(+)IL-7R(+)Lin(-)ROR gamma t(-) and c-kit(+)IL-7R(+)Lin(-)ROR gamma t(low) cells outside the CP basically remain in the gut mucosa of ROR gamma t-deficient ROR gamma t(EGFP/EGFP) mice. Consistent with these non-Lti-like c-kit(+)IL-7R(+)Lin(-) cells being gut T cell progenitors, ROR gamma t-deficient mice develop the normal number of intestinal mucosal T cells. These results clearly reassert the intraintestinal differentiation of the body's largest peripheral T cell subpopulation.