The nonintegrin receptor CD26, also known as dipeptidyl peptidase IV (DPP IV) is a transmembrane 110- to 120-kDa serine aminopeptidase glycoprotein with multiple functions, including cellular trafficking through extracellular matrix, and costimulatory potential during T cell activation, and is an influence upon T cell differentiation during their maturation in the thymus. In order to further define the expression and functional activity of this membrane exopeptidase in human thymus, we utilized a nondisruptive, cytofluorogenic assay which allowed simultaneous measurement of intracellular DPP IV activity using a fluorochrome-conjugated peptide substrate with surface staining of plasma membrane-associated T lymphocyte lineage antigens CD4 and CD8, as well as CD26. Human thymi were examined using the three-color assay, and significant differences in time-dependent DPP IV activity were found among the thymocyte subsets defined by their CD4/CD8 phenotype. In this regard, CD4(-)/CD8(-) thymocytes displayed the lowest DPP IV activity and had higher activity than the smaller-sized CD26(+) cells. Thymocytes containing greater percentages of apoptotic cells expressed lower DPP IV activity than viable cells. Thus, DPP IV appears to be upregulated as thymocytes mature and is reduced among thymocyte populations enriched for cells undergoing programmed cell death, suggesting that CD26-associated enzymatic activity is ontogenically controlled during T cell maturation and may be involved in thymic deletion of emerging clones.