Apoptosis is the common phenotype of programmed or physiologic cell death, the process used to remove excess or defunct cells during normal tissue maintenance. One of the most studied cell types with respect to apoptosis is the immature T cell from the thymus, which activates its death program in response to an enormous variety of agents. Previously, our group implicated the calcium-dependent cytosolic protease calpain as a participant in thymocyte apoptosis initiated by glucocorticoids or irradiation. We found that the calpain inhibitors N-acetyl-leu-leu-norleucinal (calpain inhibitor I) and carbenzoxy-val-phe-H (MDL 28,170) prevented dexamethasone-induced apoptosis of thymocytes; in this study, we show that two additional calpain active site inhibitors, L-3-carboxy-trans-2,3-epoxypropionyl-leu-amido-(4-guanidinio )butane ethyl ester (E64d) and carbenzoxy-leu-leu-tyr-CHN2 (ZLLY-CHN2), also prevent apoptosis in this model. Three compounds that inhibit lysosomal cysteine proteases, carbenzoxy-tyr-ala-CHN2 (ZYA-CHN2), ammonium chloride, and chloroquine, do not block apoptosis, indicating that the effect of the calpain inhibitors is not due to cross-inhibition of lysosomal proteases. In addition, I-benzyl-CH=C(SH)COOH (PD150606), a calpain inhibitor directed toward the calcium binding sites of calpain, also prevents apoptosis. Calpain is necessary for other models of programmed cell death that require new gene expression (induction models), those following treatment of thymocytes with the calcium ionophore A23187, ionomycin, or forskolin. However, two models of thymocyte apoptosis that do not require new gene expression (transduction models), those triggered by heat shock and by valinomycin, are calpain independent, as is calcium-triggered DNA fragmentation in isolated thymocyte nuclei. These experiments suggest an upstream regulatory role for calpain in a pathway to thymocyte apoptosis common to several inducers.