Current research indicates that replacing organic solvents with room-temperature ionic liquids may lead to remarkable improvements in well-known processes. Ionic liquids have already been utilized as alternative solvents in organic synthesis and catalysis, and also in electrochemistry and in separation sciences. Their wide applicability will soon result in their production on an industrial scale. Therefore, analytical methods applicable to various matrices for product control and environmental monitoring will be very much in demand. In this study, the usefulness of pi...pi interactions between alkylimidazolium and pyridinium cations and the aromatic pi...pi active moiety of the stationary phase was investigated for the selective separation and analysis of some ionic liquids. With phenyl-bonded phases, very good separations of the cations were achieved. Special attention was paid to the short-chain hydrophilic entities, known to be poorly separated on conventional reversed-phase columns. Further, the nature of the interactions occurring in the system under study was investigated by varying the content of methanol/acetonitrile used as organic modifiers in the mobile phases. The analytical method developed here is simple and reproducible, and its quantitative analytical performance was excellent. The paper also discusses the applicability of the method for monitoring degraded cations of 1-butyl-3-methylimidazolium salts obtained in the Fenton process.