In the veterinary field, their ability to regulate gene expression and their stability make miRNAs useful tools to guide breeding programs for disease resistance in many types of livestock, including pigs. Although there are currently 1043 human miRNAs in the miRBase database, only about 250 pig miRNAs have been identified so far. Initially, miRNAs in livestock such as cattle and pigs were discovered using homology searches. However, after the high-throughput detection platform was developed, high-density small RNA expression profiles could be rapidly identified using gene chips, although these were limited to the detection of known miRNAs. In recent years, the emergence of Solexa and 454 highthroughput sequencing technologies have enabled the direct sequencing of miRNAs and thus the discovery new miRNAs. Xie et al. constructed a small RNA cDNA library for 16 tissues of Silmitasertib 1009820-21-6 different pig breeds, conducted deep sequencing on the miRNA transcriptome, and obtained 437 conserved and 86 predicted porcine miRNA sequences. Following this, Xie et al. customized gene chips and identified 58 miRNAs differentially expressed in native Chinese Tongcheng pigs and the Large White exotic breed that contain different lean meat percentages. Likewise, Li et al. constructed small RNA cDNA libraries of pig tissues at different growth stages from the fetal period to adulthood, and sequenced these using the Genome Analyzer GA-I. Our main research focus is diarrhea and edema disease of weaned pigs caused by E. coli F18. Previous studies have shown that E. coli F18 cells combine with the intestinal epithelial cell receptor of piglets through surface fimbriae, and then multiply and produce toxins, leading to piglet disease. Vogeli et al. found that FUT1 gene and the epithelial cell receptor gene were closely linked, and that a G to A mutation at locus M307 of the FUT1 gene that alters the structure of the receptor could be used as a genetic marker for screening. However, no AA genotype has been detected following screening of dozens of local breeds in China. Thus, the FUT1 gene is not a suitable genetic marker for the selection of E. coli F18-resistant local Chinese pig breeds. It therefore seems that exotic breeds and Chinese local pig breeds have different resistance mechanisms to E. coli F18 infection. We previously used gene chips to screen for differential gene expression in eight full-sib pair groups of E. coli F18-sensitive and – resistant Sutai pigs bred under the same conditions. We have now constructed small RNA duodenal libraries of individual E. coli F18-sensitive and -resistant weaned piglets in full-sib pair groups and analyzed these by Illumina Solexa high-throughput sequencing to identify differentially expressed miRNAs. This provides improved database information on pig miRNAs, better understanding of the genetic basis of E. coli F18 resistance in local Chinese and exotic pig breeds, and lays new foundation for identifing new markers in E. coli F18 resistance. In this study, sequencing of small RNAs from the duodenum of E. coli F18- sensitive and -resistant individuals was done using Illumina Solexa technology, and differentially expressed miRNAs were identified. We found that more than 90% of known swine miRNAs are expressed in duodenal tissues of all weaned piglets. In addition, a large number of small RNAs had sequences consistent with miRNA structure, indicating that physiological functions of the pig intestinal tract are regulated by miRNAs. As the swine and human miRNA sequences show a high degree of homology.