The pathogenesis of tuberculosis-causing Mycobacterium bovis is largely due to its ability to enter and survive in alveolar macrophages. Its mechanism of entry, mediated by proteins encoded by mammalian cell entry (mce) genes, is important for its pathogenesis. Here we focussed on the role of the Mce4A protein in the pathogenesis of M. bovis in cattle. Cell livability decreased in a dosage-dependent manner when Mce4A proteins were used to stimulate alveolar macrophages, which suggested that the recombinant Mce4A protein significantly inhibited alveolar macrophage activity. To test whether Mce4A modulates the gene expression profile of alveolar macrophages, alveolar macrophages were stimulated by Mce4A protein and other proteins/ligands (such as MtbPPD, MbPPD, and BCG), followed by real-time RT-PCR assay for the mRNA expression level of TNF-alpha, iNOS, IL-6, and IL-12. The results showed that the expression of TNF-alpha, iNOS, and IL-6 in alveolar macrophages was up-regulated by stimulation with the recombinant Mce4A protein of M. bovis; in contrast, expression of IL-12 was unaffected. MbPPD and BCG up-regulated the mRNA expression of TNF-alpha, iNOS, IL-6, and IL-12 (P < 0.05), whereas MtbPPD stimulated the mRNA expression of TNF-alpha, IL-6, and IL-12 with no effect on iNOS. This study suggests that Mce4A proteins may induce the body's inflammation response to M. bovis and therefore may play an important role in the immune response.