An extract of Ginkgo biloba leaves (EGb) was administered by gastric probe to Wistar female rats, and urine and faeces samples were collected for 5 days and whole blood samples were withdrawn every 30 min for 6 h. After purification with SPE C18 cartridges, the samples were analysed by reversed-phase LC-diode array detection (LC-DAD) for residual flavonoid glycosides, aglycones and metabolites. No glycosides or aglycones were detected in urine, faeces or blood and extensive degradation of EGb flavonoids within 24 h was detected. Among the seven different phenylalkyl acids detected by LC-DAD, 3,4-dihydroxyphenylacetic acid (I), hippuric acid (II), 3-hydroxyphenylacetic acid (III), homovanillic acid (IV) and benzoic acid (VII) were directly confirmed by on-line mass spectrometry using an electrospray interface (ES-MS). Peaks V and VI needed to be collected and separately examined and they were found to be 3-(4-hydrophenyl)propionic acid and 3-(3-hydrophenyl)propionic acid, respectively. As further evidence, the identity of metabolites I, II, III, IV, V and VII was confirmed by co-chromatography with authentic standards.