Abstract: This experiment was designed to screen the genes of host involved Brucella intracellular infection and lay a foundation for elaborating the pathogenic mechanism. The murine macrophages were infected with Brucella melitensis 16M strains, and then the differently expressed genes of macrophages were screened with the digital gene expression profiling technology. The genes differently expressed were verified with the quantitative real-time PCR. Then the genes were analyzed with the GO Term and KEGG to screen the signals significantly enriched. There were 3 576 genes expressed significantly difference 4 hours post infection, approximately 58% genes were up-regulated. NOD-like receptor signaling pathway, lysosome pathway, Fc gamma R-mediated phagocytosis, p53 signaling pathway, apoptosis pathway and protein processing in the endoplasmic reticulum pathway were enriched. Transcriptomics profile of murine macrophages infected with Brucella melitensis 16M strain was successfully analyzed.