The chromatographic behavior of charged analytes in ion interaction chromatography (IIC) is theoretically investigated. The chemical modifications of the stationary and mobile phases in the presence of ion interaction reagent (IIR) are theoretically shown to change the partition coefficient for charged molecules. The most reliable literature experimental results concerning retention behavior of charged molecules in IIC were used to test the new theory. Retention equations are compared with those that can be obtained from the most important retention models in IIC. The present exhaustive retention model, which is well-founded in physical chemistry, goes further than the previous ones whose retention equations can be viewed as limiting cases of the present theory. The present extended thermodynamic approach reduces to stoichiometric or electrostatic retention models if the surface potential or pairing equilibria are respectively neglected. Moreover, it is able to quantitatively explain experimental evidences that cannot be rationalized by the existing retention models.