Gastrodin is a component extracted from the rhizome of Gastrodia elata, and has been shown to possess protective effects against neuron damage induced by simulated cerebral ischemia in previous studies. But its neurochemical effects on the ischemic brain had not been well studied. The present study aimed at evaluating the effects of gastrodin on the changes of transmitter amino acids in rat hippocampus during cerebral ischemia/reperfusion. Microdialysis sampling was performed during ischemia and early reperfusion periods in rats, and the glutamate and gamma-aminobutyric acid (GABA) in the dialysate were measured using high-performance liquid chromatography (HPLC). Administration of gastrodin (100 mg/kg) before ischemia significantly reduced the ischemia-induced elevation of glutamate levels during the postischemic period, increased the rise of extracellular GABA during the reperfusion periods, thus decreased the glutamate/GABA ratios during ischemia and reperfusion. These results provide insights to explain the neurochemical effects of gastrodin when applied prior to an ischemic event.