To identify specific expressed miRNAs of Neospora caninum and to investigate their expression in host cells,the samples of caprine endometrial epithelial cells(EECs)infected with tachyzoites of N.caninum at 24 and 48 h were collected.Specific expressed miRNAs of N.caninum and their in vitro expression were analyzed by using Illumina highthroughput sequencing technology and bioinformatics analysis.The effect of an up-regulated miRNA,novel3_mature,on the propagation of N.caninum in caprine EECs was also studied.The results showed that a total of 3 404 specific expressed miRNAs(155 novel predicted miRNAs)of N.caninum were identified.Of them,77(47 up-and 30 down-regulated)miRNAs were significantly differentially expressed.The consistent results were found with highthroughput sequencing by using quantitative real-time PCR analysis of seven significantly differentially expressed miRNAs randomly selected.Predictive analysis found 3 978 target genes of 61 miRNAs.Functional enrichment analysis showed that these target genes were possible involved in MAPK signaling pathway,axon guidance,focal adhesion,cAMP signaling pathway,calcium signaling pathway.Transfection of novel3_mature mimics significantly promoted the propagation of N.caninum in caprine EECs.Many specific expressed miRNAs were encoded by N.caninum and they played important roles in the propagation of N.caninum,providing a novel way to understand the intracellular survival of N.caninum.