The physiological levels of many clinically important proteins are regulated through cellular mechanisms that control the stability and translational efficiency of mRNA. These post-transcriptional processes, which play a critical role in the regulation of gene expression, depend on interactions of specific trans-acting factors with sequence elements located within the 5'- and 3'-untranslated regions (UTRs) of an mRNA. A technology platform called GEMS (Gene Expression Modulation by Small-molecules) exploits the interactions of UTR elements with the trans-acting factors, thereby specifically targeting mechanisms of post-transcriptional control. In this review we describe how this technology enables the identification of small-molecules that modulate the levels of proteins involved in disease pathogenesis.