A quantitative thymocyte regeneration assay was used to monitor the isolation of functional prothymocytes from rat bone marrow on the FACS. Two prothymocyte subpopulations were tentatively identified on the basis of their relative resistance to dexamethasone. Both populations were comprised of undifferentiated, medium-size cells that displayed large amounts of Thy-1 antigen. Simultaneous sorting of bone marrow cells according to relative low angle light scatter (size) and relative fluorescence intensity for Thy-1 resulted in enrichments of 112-fold and 260-fold, respectively, in prothymocyte activity in untreated and dexamethasone-treated bone marrow. These prothymocyte-enriched cell fractions contained or approximately 75% of total functional prothymocyte activity in bone marrow, and represented 1.1 and 0.35% of total untreated and dexamethasone-treated bone marrow cells. Using these enriched cell fractions, significant thymocyte regeneration is possible with as few as 2 X 10(4) and 1 X 10(4) bone marrow cells, respectively. The possible relationship of these functional prothymocyte subpopulations with CFU-S and with TdT-positive cells is discussed.