Integrative research has taken on the challenge of addressing questions in physiology by using novel knowledge and novel techniques. Recently, small and long non-coding RNAs have emerged as key regulators of gene expression, while next-generation sequencing technologies have revolutionized the characterization of genomes and gene expression. For a decade, it has been known that microRNAs (miRNAs) are RNAs of 18-24 bases that regulate gene expression in mammals. Here, we first describe the nature of miRNAs and the advantages of high-throughput sequencing technologies for establishing miRNA expression profiles. The hypothalamus harbours a dozen specialized areas or nuclei, the sampling of which is required to establish physiologically relevant miRNA expression profiles. MicroRNA expression profiling from single animals is also important for investigating potential genetic or epigenetic differences between individuals. Establishing a large number of miRNA expression profiles of individual hypothalamic nuclei of single rats at a cost compatible with laboratory finance can be achieved by using tagged cDNA libraries constructed from purified small RNAs and a multiplex sequencing strategy. We continue this report by surveying specificities of the different strategies that are used at present for constructing tagged cDNA libraries and provide a comparative analysis of miRNA expression profiles from hypothalamic arcuate nuclei of seven male Wistar rats.