We describe a novel technique for studying the signaling pathways that control thymocyte negative selection which maintains the essential interactions between thymocytes and thymic stromal cells. Bisected lobes from newborn mouse thymus are maintained in organ culture for up to 36 h, and the thymocytes analyzed by flow cytometry. Inclusion of [3H]inositol during culture allows measurements of phosphatidylinositol 4,5-biphosphate (PtdIns(4,5)P2) hydrolysis and inositol phosphate accumulation. Using this technique we have compared the thymocyte responses induced by anti-CD3, anti-Fas, Con A, and beta-adrenergic stimulation. We show that PtdIns(4,5)P2 hydrolysis precedes anti-CD3-induced thymocyte apoptosis, but not the apoptosis induced by anti-Fas. In contrast, Con A stimulates PtdIns(4,5)P2 hydrolysis, but does not induce thymocyte apoptosis. Anti-CD3, anti-Fas, and Con A all fail to change thymic cAMP levels, but beta-adrenergic stimulation causes a large increase in intracellular cAMP, and agents that elevate cAMP induce thymocyte apoptosis. Inhibition of protein synthesis (with cycloheximide or emetine) prevents the apoptosis induced by anti-CD3 and elevated cAMP, but not that induced by anti-Fas, whereas protease inhibition (with 3,4-dichloroisocoumarin or N(alpha)-tosyl-phenylalanine chloromethyl ketone) prevents the apoptosis caused by all of the effective stimuli. These results offer three important conclusions. First, activation of a variety of different signaling pathways can bring about thymocyte apoptosis. Second, ligation of the thymocyte TCR/CD3 complex provokes PtdIns(4,5)P2 hydrolysis, but signaling through this pathway alone does not necessarily lead to apoptosis. Third, by whichever signaling pathway the response is initiated, the activity of one or more protease enzymes appears to form an essential component in the final common pathway leading to apoptosis.