HPLC-MS using collision induced dissociation (CID) has been utilised for the identification of the C-glycosylflavone isomer pairs orientin/isoorientin and vitexin/isovitexin. HPLC-CID/MS analyses produced pseudo-MS/MS spectra that allowed the identification of the flavone C-glycosides. The efficient differentiation of isomers was performed by comparing the CID-MS/MS spectra (including exact mass measurements) of particular fragments from the C-glycoside unit. In order to illustrate some possibilities of these MS techniques, they were applied to the comparative analyses of extracts of Passiflora alata, P. edulis, P. incarnata and P. caerulea (Passifloraceae) that are employed as phytomedicines in Brazil and South America.