Baicalin and baicalein, a flavone glucuronide and its aglycone, are bioactive constituents of Scutellariae Radix with various beneficial activities. We have characterized and compared the metabolic pharmacokinetics of baicalin and baicalein in rats. Baicalein was administered intravenously and orally to rats, and baicalin was orally administered. An HPLC method was used to determine the concentration of baicalein before and after hydrolysis using beta-glucuronidase/sulfatase. The pharmacokinetic parameters were calculated by using WINNONLIN. Unpaired Student's t-test was used for statistical comparison. The result showed that after intravenous administration of baicalein, 75.7% of the dose was circulating as its conjugated metabolites. After oral administration of baicalein, absorption of baicalein itself was negligible, whereas the glucuronides/sulfates of baicalein were predominant in the plasma. When compared with intravenous bolus administration with dose correction, the absolute absorption was 40%. When baicalin was administered orally, glucuronides and sulfates of baicalein were exclusively circulating in the plasma. The relative absorption for baicalin was 65% when compared with baicalein. Profound differences of serum profile and pharmacokinetics were observed between oral baicalein and baicalin. Baicalin demonstrated significantly later time to peak concentration (t(max)) and lower peak serum concentration (C(max)) of baicalein conjugated metabolites than baicalein, indicating baicalin was absorbed more slowly and to a lesser extent than baicalein.