Abstract: Examination was made of the urinary excretion of baicalin and its isomer in rats. The urine of rats administered baicalin orally and intravenously contained two metabolites, baicalin and baicalein 6-O-glucuronide, as determined from MS n data and UV spectra. Urine samples obtained 0-48h after oral (100mg/kg) or intravenous (15mg/kg) administration of baicalin were collected and were extracted by ethyl acetate. The internal standard was quercetin and the mobile phase composed of methanol-water-formic acid (60∶40∶1, v/v). Urine samples were investigated by liquid chromatography-electrospray ion trap mass spectrometry(LC/MS n). The formation of baicalein 6-O-glucuronide suggested that baicalin partly appeared to be hydrolyzed to aglycone after absorption in the body, then excreted in the urine or bile. Total cumulative amounts of the baicalin and baicalein 6-O-glucuronide excreted in the urine at 48h following the oral administration of baicalin were approximately 1.49% and 1.19%, respectively, and total cumulative amounts following the intravenous administration of baicalin were approximately 30.80% and 0.28%, respectively. The absolute availability of baicalin in rat was 4.84% according to the amount of baicalin.