A method was developed for the analysis and characterization of quercetin and kaempferol in urine following ingestion of Ginkgo biloba tablets. The method utilized gas chromatography/negative ion chemical ionization mass spectrometry of the trimethysilyl derivatives of the flavonoids. Limits of detection for these compounds using this method were ca. 20 pg on column. Liquid chromatography with electrospray mass spectrometry in the negative ion mode was utilized to characterize the complex mixture of glycosides present in the G. biloba tablets, the limit of detection with this technique was ca. 10 ng on column.