A novel method for paralytic shellfish poisoning (PSP) toxins which is based on the chromatographic separation of the toxins using a zwitterionic (ZIC) hydrophilic interaction chromatography (HILIC) column is presented. Efficient retention of the polar PSP toxins on the ZIC-HILIC column allowed their selective and sensitive determination by the application of mass spectrometric (MS/MS) detection or as derivatives after oxidation prior to fluorescence detection (FD). Low buffer concentrations and the omission of ion-pair reagents decreased the limits of detection (LODs) by MS/MS analysis and showed a good linearity for both methods of detection. This method can be applied for the qualitative and quantitative determination of PSP toxins in various types of phytoplankton, and for the routine analysis of seafood.