The implication of the STAT6 transcription factor in several human diseases makes the regulation of its activity a topic of great biological interest. The activation of this transcription factor is tightly regulated by kinases, phosphatases, and proteases. The initial aim of this study was to investigate the utility of protease inhibitors in controlling STAT6 activation. Among all inhibitors analyzed, n-alpha-tosyl-L-phenylalanine-chloromethyl ketone (TPCK) was found to inhibit the IL-4-induced STAT6 activation. Unexpectedly, this inhibition was accompanied by a loss of STAT6 protein. Thus, TPCK promoted the loss of STAT6 by a mechanism sensitive to the serine-protease inhibitor 4-(2-aminoetyl)-benzenesulfonyl fluoride. However, the effects of TPCK seemed not to be mediated by its protease inhibitory activity since multiple protease inhibitors tested had no effect on STAT6 expression. The results found suggest that the effect of TPCK was mediated by its alkylating activity. Thus, cysteine reactive and thiol antioxidant compounds prevented the loss of STAT6 induced by TPCK. The reactivity of thiol groups on STAT6 was moreover demonstrated with biotinylated sulfhydryl-reactive compounds. Analysis of other signaling molecules indicated that STAT5, but not other STATs, Shc, or c-Rel, was also affected by TPCK, suggesting a common downregulatory mechanism for STAT6 and STAT5. These results reveal a novel mechanism of action of TPCK in inducing a selective loss of STAT proteins. These findings may have implications for diseases in which STAT proteins are involved.