MicroRNAs (miRNAs) are short (22 nucleotides) non-coding ribonucleic acid (RNA) molecules that post-transcriptionally repress expression of protein-coding genes by binding to 3'-untranslated regions of the target mRNAs. In order 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 hybridization (FISH). The expression pattern of the mature miRNAs miR-7a, miR-7b, miR-137 and miR-153 in mouse brain tissue sections was investigated. Whereas 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, suprachiasmatic, paraventricular, periventricular, supraoptic, dorsomedial and arcuate nuclei. Identical expression patterns for miR-7a was 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 (NPY)/agouti-related protein (AgRP)-containing-neurons located in the ventromedial aspect of the arcuate nucleus, but not in large pro-opiomelanocortin (POMC)/cocaine- and amphetamine-regulated transcript (CART)-containing anorexigenic neurons of the ventrolateral part of the arcuate nucleus. The limited and distinct expression of miR-7a in the CNS suggest that miR-7a has a role in post-transcriptional regulation in hypothalamic neurons. Particularly strong expression of miR-7a in neurons 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. © 2012 The Authors. Journal of Neuroendocrinology © 2012 Blackwell Publishing Ltd.