Microdialysis coupled to liquid chromatography (LC) has proven to be a valuable in vivo sampling technique for studying neurotransmitter changes in normal and ischaemic brain. However, few analytical methods have described the simultaneous determination of amino acids, relevant in stroke research, together with the nitric-oxide-related compound citrulline. Therefore, we developed a gradient LC method for the quantitative simultaneous determination of aspartate, glutamate, serine, glutamine, arginine, taurine, alanine and citrulline in dialysates of rat brain using narrowbore LC with o-phthalaldehyde-2-mercaptoethanol pre-column derivatisation and fluorescence detection. The proposed method is a thoroughly validated, fully automated and robust LC method for the determination of amino acids in a wide concentration range. The method was applied for the determination of amino acids and the citrulline/arginine ratio in the Et-1 model for focal cerebral ischaemia.