MicroRNAs (miRNAs) are a class of small non-coding RNA molecules, which are potent post-transcriptional gene expression regulators. They have been shown to participate in the regulation of numerous cellular processes, the list of which is still growing. miRNAs affect numerous targets that can be determined by direct experiments or predicted by bioinformatics approaches, and are presented in several online databases. Feasibility of miRNA for high-throughput experimentation is becoming possible due to the availability of commercially produced molecules, which are able to alter the levels of endogenous miRNAs. miRNA functional analysis will help to validate predicted targets and reveal the role of these small molecules in biological pathways. miRNAs have a high potential to be used as a new gene expression regulating reagent for microscopy based assays.