Using male and female RAG(-/-) mutant mice expressing TCR transgenes specific for MHC class I- or II-presented HY peptides, we performed quantitative and phenotypic comparisons between the TCR(+) lymphocytes present in the lymphoid organs and the gut mucosa in euthymic versus athymic (nude) animals. These comparisons suggest that only a minority of the TCR(+) CD8alpha alpha (+) intraepithelial lymphocytes (IEL) of the transgenic euthymic mice originate from hematopoietic precursors acquiring a TCR in the gut wall, while a majority of these CD8alpha alpha(+) IEL appear to be of thymic origin (as were all TCR(+) CD8alpha beta (+) or CD4(+) in any location); these last cells are released from the thymus as double-negative thymocytes, which are at a more immature stage (CD44(+)CD25(+)) in female mice than in males (CD44(-)). In view of previous observations that in non-transgenic athymic mice the CD8alpha alpha (+) TCR(+) IEL populations are also markedly reduced quantitatively, the possibility of a thymic contribution to these ontogenically peculiar populations may also exist in normal mice. At which stage of differentiation such precursors might leave the thymus of normal adult mice remains to be explored.