Gene expression profiling using a bovine-specific cDNA microarray system has revealed a subset of genes (6) activated by exposure of bovine peripheral blood mononuclear cells to live M. paratuberculosis. Subsequent analysis gene expression by real-time PCR and Northern blot hybridization has suggested that several of these genes are strongly activated in macrophages by uptake of E.coli within 60 minutes of phagocytosis. The kinetics of gene expression when M. paratuberculosis is phagocytosed appear to be severely delayed relative to E.coli. Our results suggest that M. paratuberculosis is capable of entering macrophages in a manner that prevents the immediate activation of these cells and may have implications for how M. paratuberculosis and other mycobacteria survive in host macrophages.