The T cell repertoire is shaped by both positive and negative influences. T lymphocytes that express the V beta 6 variable region are positively selected in the thymus by cells expressing major histocompatibility complex (MHC) class II E molecules. To identify these cells, we have quantitated V beta 6+ T lymphocytes in a set of transgenic mice showing variant patterns of E expression in the thymus. We demonstrate that class II molecules must be expressed on epithelial cells of the cortex for positive selection to occur. Using a direct assay of unmanipulated thymocytes, we show that positive selection is manifest only as a rather late event in thymocyte differentiation, after the maturation of cortical double-positives into single-positives.