Liquid Chromatography-Ion Trap Mass Spectrometry with an atmospheric pressure chemical ionization (APCI) interface in the negative and positive-ion modes in parallel to UV-diode-array detection (DAD), was applied for the rapid detection/characterization in crude extracts of the water-soluble antioxidant phenolics from Helichrysum stoechas. APCI-MS provides unequivocal molecular weight data of these compounds and useful information about their structures (diagnostic fragments ions), which were confirmed by the UV-DAD fingerprints. This combined approach allows the identification of ten constituents, including the three naturally occurring isomers of caffeoylquinic acid (CGAs), namely neo-chlorogenic acid, chlorogenic acid and crypto-chlorogenic acid, 2 isomeric dicaffeoyl quinic acids, 2 isomeric naringenin glucosides, quercetin, kaempferol and apigenin glucosides and a tetrahydroxychalcone-glucoside. The water-soluble extract from H. stoechas, standardized in both total polyphenol and kaempferol-3-glucoside content, exhibits strong antioxidant activity in vitro when tested in both artificial membrane systems (phosphatidylcholine liposomes) and in a cell model (rat erythrocytes).