Aptamers are artificial nucleic acid (single-stranded DNA or RNA) ligands that bind to certain targets with high specificity. They have numerous advantages, including satisfactory stability, ease of chemical modification, and the ability to be synthetically created. Further, their low immunogenicity means they are often a more promising choice than antibodies. Quantification of new aptamer-target interactions is crucial for selection of appropriate sequences and further research. Capillary electrophoresis (CE) may be a suitable technique for determining the basic parameters of such biomolecular interactions. Today, several methods for studying binding parameters using the CE technique exist. In the case of aptamers, the NECEEM (non-equilibrium capillary electrophoresis of equilibrium mixtures) method is widely used. Based on fundamental parameters, such as peak area and migration time, obtained from a single electropherogram, the degree and strength of binding can be evaluated. Undoubtedly, further research into aptamers must be pursued to extend the frontiers of their bioapplications. Thus, the presented technique provides a highly efficient and versatile platform for the development and assessment of new ligands. © 2018 Nova Science Publishers, Inc.