The separation of three flavonoids, kaempferol, quercetin and luteolin, by capillary zone electrophore-sis with three 1-ethyl-3-methylimidazolium ionic liquids (ILs), namely chloride, hydrogen sulfate andtetrafluoroborate salts, under non-aqueous conditions using acetonitrile as solvent was investigated.Depending on the IL, the three flavonoids can be separated under positive voltage with a low IL concentra-tion and negative voltage with a high IL concentration. The separations are based on heteroconjungationbetween the IL anions and the analytes. The heteroconjungation between the anions of the ILs and theanalytes is proton sensitive and only a very small amount of protic solvents, such as methanol, addedinto the electrolyte solution can harm the separation, but higher IL concentrations can overcome thishigher amount of protic solvents. Using a high concentration of IL in the sample was used to enhancethe flavonoid solubility by as much as 10, overcoming the problem of the low solubility during NACEanalysis with ACN as the solvent. Finally, kaempferol, quercetin and luteolin in Semen Plantaginis wereanalysed by nonaqueous capillary electrophoresis with low concentration of the hydrogen sulfate ionicliquid with excellent results.