Analytical capillary zone electrophoresis (CZE) conditions including concentration, pH value and nature (complexing or non-complexing) of the running buffer with or without the addition of methanol, capillary temperature and applied voltage, were studied in order to optimize the separation and resolution of a mixture of 13 C-glycosylflavones and one flavone O-glucoside. Factors primarily responsible for differences in electrophoretic mobility of flavone C-glycosides are identical to those defined from the separation of flavonoid O-glycosides, i.e. number and position of the free hydroxy groups on the flavone skeleton, and number and type of attached sugar groups. Nevertheless, an increase in the pH value from 9 to 10 of the borate running buffer affects the elution order: such an increase induces greater relative electrophoretic mobilities of C-glycoside derivatives with a free hydroxy group at C-4' compared with those of luteolin Cglycoside derivatives. This change in the migration order could be explained both by a decrease of the net charge linked to an increase and stability of the borate-luteolin complexation and by an increase in molecular size. Moreover the 6-C-glycosylflavones present electrophoretic mobilities lower than their homologous 8-C-glucosyl isomers. Finally, the study of C-glucosylflavones from 18 different samples of Passiflora incarnata by CZE shows a great variability in the qualitative composition.