Abstract: Encephalomyocarditis virus (EMCV) can infect humans and many animals. This genome-wide expression profile could contribute to exploring the association between gene expression and pathogenicity, and revealing the molecular mechanism after infection. N2a cells were infected usingEMCV BD2 strain. The cells were collected 7 hours after infection, total RNA was extracted from EMCV infected group and normal control group, respectively. Microarrays were hybridized with labeled ds-cDNA in a NimbleGen Hybridization System. Following hybridization, washing was performed. After being washed, the slides were scanned. The data of the differentially expressed genes obtained from scanning were identified and analyzed by applying bioinformatics method. Real-time FQ-PCR was performed to corroborate the results obtained with the microarray analysis. The results showed that a total of 21 143 genes were identified as differentially expressed genes at 7 hours after EMCV infection. These genes are involved in many vital functional classes, including immune response, inflammatory response, apoptosis, defense response, signal transduction. And the differentially expressed genes associated with interferon were significantly up-regulated, suggesting that interferon plays an important role in host antiviral infection. The pathway analysis demonstrated that the most significant pathways were associated with PI3K-Akt signaling pathway, MAPK signaling pathway, chemokine signaling pathway, cytokine, TLR, TCR, RLR and Jak-STAT signaling pathway. These results indicate that the host initiates a different strategy to activate immunological and inflammatory reaction to fight infection after EMCV infection. The changes of 10 differentially expressed genes detected by Real-time FQ-PCR were consistent with those predicted by microarray analysis.