A total of 148 miRNAs were differentially expressed in the uterus from letrozole-induced rat model compared with the control. The differentially expressed miRNAs were predicted to target a large set of genes with different functions. Pathway analysis supported that these miRNAs were involved in different signaling pathways. MiRNAs differentially expressed in rat uterus with PCOS might be involved in the etiology and pathophysiology in the uterus of PCOS.