Microwave-induced adverse health outcomes have been gaining much attention in recent years. The hippocampus is sensitive and vulnerable to microwave exposure. Studies from our group and others showed that microwave-induced structural and functional injury of hippocampus, accompanied with alteration of gene and protein expression. It has been demonstrated that microRNAs (miRNAs) were involved in the physiological and pathological processes of brain. In this study, the miRNAs expression profiles of microwave-exposed hippocampus were detected by microarray analysis and verified by real-time polymerase chain reaction (PCR). At 7 days after 30 mW/cm(2) microwave exposure, the expression of 12 miRNAs increased, while other 70 miRNAs decreased in rats' hippocampus. However, most of miRNAs restored to normal levels at 14 days after exposure, only two upregulated miRNAs and 14 downregulated miRNAs were detected. Gene transcription, neuroprotection and receptors function related target genes were predicated by miRDB, miRbase and miRanda. Moreover, these differentially expressed miRNAs were involved in brain-related signaling pathways, such as synaptic vesicle cycle, long-term depression, calcium signaling and neurotrophin signaling pathways. In conclusion, we successfully characterized the miRNA profiles in microwave-exposed hippocampus, and that will be helpful to clarify the molecular mechanism and provide potential therapeutic targets.