The role of the thymus in the induction of tolerance to peripheral antigens is not yet well defined. One impending question involves how the thymus can acquire the diversity of peripheral nonthymic self-Ags for the process of negative selection. To investigate whether peripheral Ags are synthesized in the thymus itself, we have determined the expression of a panel of circulating and cell-bound peripheral Ags, some of which are targets of autoimmune diseases, at the mRNA level in total thymic tissue and in its main cellular fractions. Normalized and calibrated RT-PCR experiments demonstrated the presence of transcripts of nonthymic self-Ags in human thymi from 8 days to 13-yr-old donors. Out of 12 glands, albumin transcripts were found in 12; insulin, glucagon, thyroid peroxidase, and glutamic acid decarboxylase (GAD)-67 in six, thyroglobulin in five, myelin basic protein and retinal S Ag in three, and GAD-65 in one. The levels of peripheral Ag transcripts detected were age-related but also showed marked interindividual differences. Cytokeratin-positive stromal epithelial cells, which are a likely cellular source for these, contained up to 200 transcript copies of the most expressed peripheral Ags per cell. These results implicate the human thymus in the expression of wide representation of peripheral self-Ags and support the view that the thymus is involved in the establishment of tolerance to peripheral Ags. The existence of such central mechanism of tolerance is crucial for the understanding of organ-specific autoimmune diseases.