Staphylococcal enterotoxins are potent T cell mitogens. Recent studies have shown that the binding of these toxins to class II MHC molecules on accessory cells is essential for the stimulation of T cells which bear specific V beta segment of TCR. In the present study we show that i.v. administration of staphylococcal enterotoxin B (SEB) results in an enlargement of spleen and lymph nodes but causes thymus atrophy. Elimination of CD4+CD8+ cells predominantly accounted for the shrinkage of thymus, and the lowest level of this cell population was reached 4 days after SEB injection. Furthermore, this decrease in CD4+CD8+ cells was accompanied by a relative increase in the percentages of CD4+CD8-, CD4-CD8+ and CD4-CD8- cells, whereas their absolute numbers actually reduced on day 4. The thymus shrinkage involved apoptosis which was characterized by DNA fragmentation and morphologic changes. The depletion of Thy-1 high, TCR-alpha beta low and TCR-alpha beta intermediate cells also occurred with a kinetic correlated to the reduction of CD4+CD8+ cells. Our results further showed that the percentages of V beta 8+ cells reduced 12 h post SEB injection, increased after 2 days, and decreased again thereafter. SEB thus causes both apoptotic and stimulative effects in the thymus. Apparently, the tremendous loss of double-positive cells (greater than 90% in cell number on day 4) is not simply due to the reduction of V beta 8+ cells, the possible modulatory effect of other factors or hormones which may play a role in the cell death is discussed.