A new, sensitive, and selective high-performance liquid chromatography-tandem mass spectrometric method (HPLC-MS/MS) has been developed for the quantification of six flavonoids (sophoricoside, genistin, genistein, rutin, quercetin, and kaempferol) in rat bile and urine. The sample pretreatment was simple by liquid-liquid extraction. Sulfamethalazole was used as internal standard (IS). During method development, the effect of extraction volume, mobile phase composition, column temperature, and injection volume were varied to optimize sensitivity and achieve a run time as short as possible. Chromatographic separation was accomplished on a C18 column with a simple linear gradient elution within 9 min. Full validation of the assay was in accordance with the requirement of the validation of the method in vivo and implemented including specificity, linearity, accuracy, precision, recovery, and matrix effect. This is the first report on determination of the major flavones in rat bile and urine after oral administration of Fructus Sophorae extract. The method has been used successfully in excretion studies of six major flavonoids in rat bile and urine.