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One of the current trends in the development of ion chromatography (IC) is associated with a growing number of applications on analysis of very complex samples. There are three main strategies to be considered for the successful separation of complex mixtures of ions. This includes an increase of column efficiency by using fine particles of ion-exchangers as low as 2.5 micron size or monolithic ion-exchange columns and exploitation of elevated power of multidimensional separations. Nevertheless, the ion-exchange selectivity remains a key factor for the successful IC analysis of samples containing many different ions or samples with excessive concentration of one or few ions over target analytes. Usually electrostatic attraction forces between charged surface of ion-exchanger and counter-ions are considered as the only type of interactions responsible for the retention of analytes in IC. At the same time, the impact of other specific interactions cannot be ignored for the selection of right IC columns and optimisation of eluent composition in IC separations. This includes coordination or complexing interactions in the separation of alkaline-earth and transition metal cations, electrostatic repulsions occurring in zwitterion exchangers, hydrogen bonding in separation of multi- element anions in eluents containing an elevated concentration of organic solvents and, finally, hydrophobic interactions in separation of organic ions. The effect of above mentioned secondary equilibria on separation selectivity will be considered for various IC modes and groups of analytes.