The induction of apoptosis by glucocorticoids in isolated thymocytes has been studied extensively. However, it is not known whether or not the same changes occur after in vivo glucocorticoid treatment. In order to investigate this, we have studied the changes occurring in thymocytes isolated from rats, from 2-24 hr after a dose of dexamethasone (1 mg/kg), which caused 50% thymic atrophy. Thymocytes were separated into four fractions by isopycnic Percoll gradients. A loss of cells occurred within 2-8 hr, primarily in only one of the two major fractions of normal thymocytes. This loss of normal thymocytes coincided with the appearance of small dense cells with characteristic features of apoptosis including condensed chromatin, increased DNA fragmentation, internucleosomal DNA cleavage and a "hypodiploid" peak on flow cytometric analysis. Striking differences occurred in the cellular composition of the different Percoll fractions with time. Initially (up to 4 hr), the pattern of changes occurring in vivo resembled those found in vitro. However, at later times, the complex fate of apoptotic cells in vivo, such as phagocytosis, are not observed in the in vitro studies.