The set-up of an on-line method for coupling nonaqueous electrokinetic chromatography (NAEKC) and electrospray ionization mass spectrometry (ESI-MS) is presented. It allows the use of the single-isomer derivative anionic cyclodextrins heptakis(2,3-di-O-methyl-6-O-sulfo)-beta-cyclodextrin (HDMS-beta-CD) and heptakis(2,3-di-O-acetyl-6-O-sulfo)-beta-cyclodextrin (HDAS-beta-CD) for chiral and achiral separations of positively charged analytes. The effect of the cyclodextrins (CDs) on the MS signal intensities of model compounds was studied. When a voltage is applied over the CE capillary, the overall mobility of the CDs is towards the inlet vial preventing CDs from entering the ion source. However, the sodium counter ions of the CDs still enter the ion source and appeared to cause ionization suppression. Nevertheless, significant analyte signals could still be detected with detection limits in the sub-microg/ml. System parameters such as sheath liquid composition and flow rate, nebulizing gas pressure, capillary position in the sprayer and the drying gas flow and temperature were studied and optimized. The selection of a relatively low nebulizing gas pressure appeared to be important to achieve optimum sensitivity. The chiral selectivity of the NAEKC-ESI-MS system could be improved by addition of camphorsulfonate to the background electrolyte. Using mixtures of drugs and drug-related compounds, the NAEKC-ESI-MS system is shown to offer potential for (chiral) drug profiling.