Background Brain hypoplasia and mental retardation in Down syndrome (DS) can be attributed to a severe and selective disruption of neurogenesis.Secondary disruption of the transcriptome,as well as primary gene dosage imbalance,is responsible for the phenotype.MicroRNA (miRNA) expression is relatively abundant in brain tissue.Perturbed miRNA expression might contribute to the cellular events underlying the pathology in DS.Methods MiRNA expression profiles in the cerebrum of Ts65Dn mice,a DS model,were examined with a real-time RT-PCR array.MiRNA target gene expression was detected by real-time quantitative PCR and West blotting.Based on the prediction of their cerebrum-specific targets,the functions of the misregulated miRNAs were annotated by Gene Ontology (GO) enrichment analysis.Results A total of 342 miRNAs were examined.Among them,20 miRNAs showed decreased expression in the brains of Ts65Dn mice,and some of these belonged to the same family.Two known targets of the miR-200 family,Lfng and Zeb2,were specifically selected to compare their expression in the cerebrum of Ts65Dn mice with those of euploids.However,no significant difference was found in terms of mRNA and protein expression levels of these genes.By enrichment analysis of the cerebrum-specific targets of each miRNA,we found that 15 of the differential miRNAs could significantly affect target genes that were enriched in the GO biological processes related to nervous system development.Conclusion Perturbed expression of multiple functionally cooperative miRNAs contributes to the cellular events underlying the pathogenesis of DS.