We have taken advantage of an extensive panel of mAb directed to thymic epithelial and nonepithelial stromal cells to examine the expression of these Ag from day 16 of gestation through 6 mo of age in NZB(H-2d), NZB.H-2b, NZB.H-2bm12, C57BL/6(H-2b), and C57BL/6.H-2bm12 mice. In addition, by triple color flow cytometry we have examined the expression of cell surface markers defining distinct stages of intrathymic T cell maturation. New Zealand mice demonstrated three abnormalities. MTS 10 normally stains thymic medullary and subcapsular epithelium. However, New Zealand mice demonstrated striking irregular medullary epithelial cell shape whereas their subcapsular epithelium remained normal. Moreover, New Zealand mice, unlike controls, were found to have MTS 10+ epithelial cells within the cortex. Additionally, MTS 39 and MTS 44, which normally stain reticular cortical epithelium, produced a striking different staining pattern in New Zealand mouse thymus, including the presence of large cortical epithelial cellfree regions, so-called "cortical holes." MTS 33 normally stains cortical thymocytes but in New Zealand mice, there was a severe decrease of MTS 33+ cells. There was also an increase of CD3lowCD4+CD8+ cells in NZB mice, which may include many predeletion thymocytes. Finally, there was a significant increase of CD3highCD4+CD8- cells in NZB.H-2bm12 and C57BL/6.H-2bm12 mice compared with NZB.H-2b and C57BL/6(H-2b) mice. We postulate that these microenvironmental alterations in NZB mice contribute to and reflect altered T cell differentiation, thereby predisposing them to autoimmune disease. Moreover, the increased proportion of CD3highCD4+CD8- cells associated with the H-2bm12 mutation may be involved in the remarkably different profiles of disease between NZB.H-2b and NZB.H-2bm12 mice.