MicroRNAs (miRNAs) are another interest of small, non-coding RNAs, which regulate gene expression at post-transcriptional level in a sequence-specific manner. Recent researches demonstrate that miRNAs play important roles in innate immune response at various phases in vertebrates. In order to eliminate pathogens such as virus, miRNAs are crucial molecules in signaling of innate immune, and also in directly interfering in virus replication, therefore, miRNA may work as one important aspect of classical innate immune response against pathogenic microorganism. Meanwhile, pathogenic microorganism, especially viruses, can encode miRNA or regulate the miRNAs expression in host cells to disturb the expression of many immune associated genes directly and/or indirectly, so that they can escape from immune attacking. So, pathogenic microorganism and their hosts might fight with each other at miRNA level immediately after infection in the earliest phase.