The Mycobacterium tuberculosis sigE gene encodes a sigma factor that is a member of the extracytoplasmic function subfamily of sigma factors. Using RT-PCR we demonstrated that sigE is expressed in M. tuberculosis bacilli during growth in human macrophages beginning after 30 min but before 6 h after infection through at least 5 days after infection, but that sigE is not expressed by M. tuberculosis bacteria during growth in Middlebrook 7H9 broth medium. However, sigE expression can be induced by treatment of broth cultures with hydrogen peroxide. Further, sigE is not expressed by M. tuberculosis bacilli during attachment or growth in type II pneumocytes. Using a green fluorescent protein (GFP) reporter gene fused to the sigE promoter, we observed induction of GFP expression following macrophage infection. Western blotting confirmed that sigE protein expression correlated with mRNA expression in induced systems. Analysis of the region of the M. tuberculosis genome encoding sigE suggested it is part of an operon consisting of sigE-orf1-htrA-orf2. The data presented in this report showed that sigE is differentially expressed by M. tuberculosis bacilli in macrophages and might play a role in the pathogenesis of this organism.