Premature ovarian failure (POF) contributes to amenorrhoea, infertility, early onset of menostasia and osteoporosis. This study profiled differentially expressed miRNAs for association with POF development. Ovarian tissue samples from 4-vinylcyclohexene diepoxide (VCD)-induced rat POF and normal rats were profiled for differentially expressed miRNAs using miRNA microarrays. A total of 63 miRNAs were up-regulated and 20 miRNAs were down-regulated in rat POF tissues versus the control tissues. qRT-PCR verified some of these altered miRNAs, i.e. miR-29a and miR-144 were down-regulated in POF tissues, which may target expression of PLA2G4A that is involved in prostaglandin biosynthesis, whereas miR-27b and miR-190 were up-regulated in POF tissues by negative control of PAPPA and CCL2 expression, respectively, both of which have been shown to relate to response to hormone stimulus. Moreover, the up-regulated miR-151 and miR-672 can also target expression of TNFSF10 and FNDC1, which have been shown to positively regulate cell apoptosis. Profiling of differentially expressed miRNAs in POF provided a novel insight into the molecular events involving the role of miRNAs in POF development with specific emphasis upon miR-27b, miR-190, miR-151, miR-672, miR-29a and miR-144.