The role of antigen presenting cells (APC) in T cell clonal deletion was investigated by culturing murine thymic lymphocytes with the superantigen staphylococcal enterotoxin B (SEB) in the absence or presence of APC. As the APC, we used B lymphoma cell lines A20.2J and BAL17.2, both expressing MHC class II antigens at high levels. SEB reactive V beta 8+ cells were deleted only when A20.2J cells were used as APC. By using thymocytes from transgenic mice carrying a TCR beta chain transgene, it was further shown that the deletion occurred at the CD4+CD8+ stage. The other cell line, BAL17.2, failed to induce clonal deletion, although this cell line was able to stimulate the proliferative response of SEB-primed T cells. The activity of A20.2J cells to induce clonal deletion was completely abolished by fixation with paraformaldehyde, whereas the same treatment kept the ability of this cell line to induce the proliferative response of non-primed as well as SEB-primed T cells. It was further shown that the deletion was abolished by the addition of anti-MHC class II but not anti-B7 mAb in the culture. These results provided explicit evidence that a signal(s) from APC, which is distinct from that required for primary or secondary proliferative response of mature peripheral T cells, is involved in clonal deletion of thymic immature T cells.