Carbohydrate differentiation antigens (CT antigens) which previously had been shown to be associated with cytotoxic T cells were found at high levels on intestinal intraepithelial lymphocytes (IEL) and on the intestinal epithelium. Histological examination of intestinal sections demonstrated that the CT1 MAb defined epitopes on IEL and on epithelial cells located in the base of the villi crypts. The CT2 MAb reacted with IEL but also bound to the majority of cells in the intestinal epithelium. When isolated intestinal cell populations were analyzed by flow cytometry, two major size classes of cells were evident. The smaller cells, corresponding to lymphocytes, were primarily Lyt-2+, with a high proportion expressing CT antigens. Another differentiation antigen defined by the MAb J11d was absent from IEL, indicating that those IEL of T cell origin are likely to be mature because thymocytes, but not peripheral T cells, express the J11d antigen. Two-color fluorescence analysis indicated that the CT determinants were present on the Thy-1+, Lyt-2+, and the Thy-1-, Lyt-2+ subsets of IEL. However, the small percentage of L3T4+ IEL were CT-, further supporting our previous demonstration of a correlation between CT expression and Lyt-2 expression. Interesting phenotypic characteristics of IEL other than CT antigen expression were also detected. IEL did not express the MEL-14 lymphocyte homing receptor, and the cell surface level of LFA-1 was significantly lower than that of other peripheral lymphocytes. It was also shown that a small percentage of IEL express a T cell receptor allotypic marker, indicating that at least some of the cells are mature in terms of T cell receptor gene rearrangements. The large intestinal cells, although CT+, were not hematopoietic in origin because they were T200- and were shown by using chimeric mice not to be bone marrow-derived. In contrast to previously reported results, the cytotoxic activity of IEL was negligible with detectable lysis against NK-sensitive cells and other tumor cells, being observed in only one of seven experiments. Thus, the expression of the CT determinants was not indicative of cytotoxic ability, as previously suggested. The presence of specific carbohydrate residues on the cell surface of a subset of lymphocytes in an anatomically distinct immune compartment suggests that a unique differentiation pathway is followed by these cells.