Interest in ionic liquids for their potential in different chemical processes is constantly increasing, as they are claimed to be environmentally benign - excellent, nonvolatile solvents for a wide range of applications. The wide applicability of these compounds also demands reliable, relatively simple and reproducible analytical techniques. These methods must be applicable not only to different technical or natural matrices but also to the very low concentrations that are likely to be present in biological and environmental systems. In this review, therefore, methods for separating and analysing imidazolium- and pyridinium-type ionic liquids in aqueous matrices using high performance liquid chromatography ( HPLC) and capillary electrophoresis (CE) are examined. The techniques for identifying ionic liquids are meant primarily to track the concentrations of ionic liquids as residues not only in products and wastes but also in biological or environmental samples. The application of hyphenated techniques in this field is intended to selectively separate the quaternary entity from other cationic and non-ionic species present in the matrix, and to enable its fine-scale quantification. Nowadays, methods developed for cation analysis are based mostly on reversed-phase high-performance liquid chromatography, ion chromatography, ion-pair chromatography and capillary electrophoresis, where various buffered mobile phases are used.