Apicultural products have been widely used in diet complements as well as in phytotherapy. Bee pollen from Echium plantagineum was analysed by liquid chromatography-photodiode-array coupled to ion trap mass spectrometry (HPLC-PAD-MSn) with electrospray ionisation interface. The structures have been determined by the study of the ion mass fragmentation, which characterizes the interglycosidic linkage in glycosylated flavonoids and differentiates positional isomers. Twelve non-coloured flavonoids were characterized, being kaempferol-3-O-neohesperidoside the major compound, besides others in trace amounts. These include quercetin, kaempferol and isorhamnetin glycosides, with several of them being isomers. Acetylated derivatives are also described. This is the first time that non-coloured flavonoids are reported on this pollen, with MS fragmentation proving to be most useful in the elucidation of isomeric structures.