We have studied the cellular basis for differential expression of the Ly-6A/E alloantigen on T cells obtained from mice of the Ly-6a (10-20% Ly-6A/E+) and Ly-6b (50-60% Ly-6A/E+) haplotypes. During T-cell ontogeny only a small fraction (less than 12%) of thymocytes expressed Ly-6A/E. By 4 weeks of age adult levels of Ly-6A/E bearing lymphocytes were seen in peripheral lymphoid tissue. Immunohistochemical studies of the thymus revealed that Ly-6A/E+ cells were located predominantly in the medulla with small clusters of Ly-6A/E+ cells throughout the cortex. Consistent with this result, phenotypic studies showed that in the adult thymus the majority of Ly-6A/E expression was on mature CD4+CD8- and CD4-CD8+ cortisone-resistant and precursor CD4-CD8- thymocytes. However, a much higher percentage of CD4+CD8- and CD4-CD8- thymocytes as well as CD4+CD8- peripheral T cells expressed Ly-6A/E from Ly-6b mice. Furthermore, although gamma interferon induced increased Ly-6A/E expression in certain thymocyte and T-cell subsets, this induction functioned preferentially for cells obtained from Ly-6b mice. Studies using F1 hybrid mice (Ly-6a x Ly-6b) indicated that the "basal" level of Ly-6A/E expression on these subsets appeared to be under codominant genetic control, whereas gamma interferon-induced regulation of Ly-6A/E expression appeared to be under dominant genetic control. Collectively, these results suggest that the expression of Ly-6A/E on a particular T-cell subset is established in the thymus and is a stable characteristic of each haplotype. In addition, the low levels of Ly-6A/E expression for the Ly-6a haplotype appear to be partially due to the inability of the majority of resting CD4+ T cells to express Ly-6A/E and to the relatively poor induction of this protein by gamma interferon.