A liquid chromatography/tandem mass spectrometry (LC–MS/MS) method has been established for the rapid and reliable determination of γ-aminobutyric acid (GABA) and glutamate in brain microdialysates. The microdialysis samples were analysed using a HILIC (hydrophilic interaction liquid chromatography) column, which is able to retain the polar amino acid neurotransmitters. The mobile phase consisted of a binary gradient elution profile comprising 0.1% formic acid in water and acetonitrile. GABA, glutamate as well as the respective internal standards [D6]-GABA and [D5]-glutamate were detected by a triple quadrupole mass spectrometer in the positive electrospray ionisation mode within a running time of 3 min. The linearity ranged from 1 nM to 10 μM for GABA and 10 nM to 10 μM for glutamate. The limit of quantitation was found to be 1 nM for GABA and 10 nM for glutamate (injection volume 10 μl). The present LC–MS/MS method was compared to the classical method for analysis of GABA and glutamate using high performance liquid chromatography (HPLC) and fluorescence detection (FD). Eventually, the feasibility of the LC–MS/MS method was demonstrated using in vivo microdialysis in rats by monitoring changes of the extracellular concentrations of GABA and glutamate in the globus pallidus following stimulation with potassium.