MicroRNAs (miRNAs) are short (∼22 nucleotides) noncoding RNA molecules that post-transcriptionally repress the expression of protein-coding genes by binding to 3′-untranslated regions of the target mRNAs. To identify miRNAs selectively expressed within the hypothalamus, a part of the brain that controls vital bodily functions, we employed locked nucleic acid (LNA)-fluorescent in situ hybridisation (FISH). The expression pattern of the mature miRNAs miR-7a, miR-7b, miR-137 and miR-153 in mouse brain tissue sections was investigated. Although all studied miRNAs were present in the hypothalamus, miR-7a, was the only miRNA found to be enriched in the hypothalamus, with low or no expression in other parts of the central nervous system (CNS). Within the hypothalamus, strong miR-7a expression was distinct and restricted to some hypothalamic nuclei and adjacent areas. miR-7a expression was particularly prominent in the subfornical organ, as well as the suprachiasmatic, paraventricular, periventricular, supraoptic, dorsomedial and arcuate nuclei. Identical expression patterns for miR-7a were seen in mouse and rat hypothalamus. By combining LNA-FISH with immunohistochemistry, it was shown that miR-7a was preferentially present in small orexigenic neuropeptide Y/agouti-related protein-containing-neurones located in the ventromedial aspect of the arcuate nucleus but not in large pro-opiomelanocortin/cocaine- and amphetamine-regulated transcript-containing anorexigenic neurones of the ventrolateral part of the arcuate nucleus. The limited and distinct expression of miR-7a in the CNS suggests that miR-7a has a role in post-transcriptional regulation in hypothalamic neurones. Particularly strong expression of miR-7a in neurones located in the ventromedial division of the arcuate nucleus, a subregion with a weak blood–brain barrier, raises the possibility that miR-7a is influenced by circulating hormones and is a regulator of the genes involved in body weight control.