Scutellarin, a flavonoid glycoside, is the primary active ingredient in breviscapine that is a mixture of flavonoid glycosides extracted from a Chinese herb Erigeron breviscapus (Vant.) Hand.-Mazz. The pharmacokinetics of scutellarin and its aglycone conjugated metabolites after intraperitoneal injection and oral administration of breviscapine was investigated in rats. The plasma concentration of scutellarin and scutellarein conjugates in serial samples was measured by validated high-performance liquid chromatography methods. The pharmacokinetic results indicated that scutellarin underwent rapid and extensive biotransformation in vivo. After intraperitoneal injection, scutellarin was absorbed rapidly. The profiles of scutellarin and scutellarein conjugates were fitted to a two-compartment open model. Scutellarin and scutellarein conjugates showed a similar time course. No significant difference in tmax, t0.5(alpha) and t0.5(beta) was observed between scutellarin and scutellarein conjugates (p>0.05). After oral administration, fluctuations were observed in the concentration-time profiles of both scutellarin and scutellarein conjugates and the pharmacokinetics could not be explained by classical compartment model. The relative bioavailability of oral administration was very low, 10.67 % +/- 4.78% for scutellarin and 7.92% +/- 1.90% for scutellarein conjugates.