Clonogenic repopulation of the thymus of thymus-homing bone marrow cells leads to intrathymic populations representing all four major Lyt-2- and L3T4-defined phenotypes. Although all four phenotypes may be represented in a single clone, quite often a striking bias in the proportion of L3T4 single positive to Lyt-2 single positive cells may exist within a clone, but not in the host thymocytes in general. Because at any one time these clones may be located in specific subregions of the thymus (specifically cortex only, medulla only, or cortex and medulla), we propose the hypothesis that different microenvironments in the thymus might, in fact, be responsible for the predominant maturation of different single positive mature thymic subsets.