Gastrodin is a bioactive constituent of rhizome in Gastrodia elata Blume (Orchidaceae) The aim of this study is to develop a rapid and sensitive liquid chromatographic method coupled to microdialysis sampling system to measure the unbound of gastrodin in rat blood, brain and bile. Microdialysis probes were simultaneously inserted into the jugular vein, brain striatum and bile duct of each anesthetized rat for sampling after the administration of gastrodin (100 or 300 mg kg(-1)) through the femoral vein. Separation of unbound gastrodin from various biological fluids was applied to an RP-select B column (250 mm x 4.6 mm i.d., 5 microm). The mobile phase consisted of acetonitrile-50 mM potassium dihydrogen phosphate buffer-triethylamine (5:95:0.1, v/v/v, adjusted to pH 2.5 with orthophosphoric acid) with a flow rate of 1 mL min(-1). The UV detector wavelength was set at 221 nm. Fifteen minutes after the administration, the gastrodin reached the peak concentration in brain and bile. In addition, the results indicate that gastrodin penetrates the blood-brain barrier (BBB) and goes through hepatobiliary excretion.