High-performance liquid chromatography (HPLC) coupled with UV photodiode-array detection and electrospray ionization mass spectrometry was developed for the simultaneous analysis of caffeic acid derivatives and alkamides in the roots and extracts of Echinacea purpurea. Caffeic acid derivatives and alkamides produced very abundant peaks in the total ion current chromatogram during negative and positive cone voltage switching. Cichoric acid and the isomer pair, dodeca-2E,4E,8Z,10E/Z-tetraenoic acid isobutylamide, were used as a standard for quantification of caffeic acid derivatives and alkamides in E. purpurea. This novel method surpasses previously published ones in product quality control and providing the HPLC chromatographic fingerprints of biological active components in E. purpurea.