Trace amount of free amino acids in brain microdialysates was separated and determinated with derivative of fluorescein isothiocyanate (FITC) using the home-made microdialysis probes and biochemical sampling unit for living animal as well as capillary electrophoresis system with intensified charge-coupled device(ICCD)-laser induced fluorescence detector. The concentration of free amino acids in microdialysates was 10^-8～10^-6 mol/L with 5 μl sample. The change of free amino acids was monitored in vivo in the hippocampus of freely moving rats before and after operational learning. These experiments suggest that the sampling and determination system can be used for analysis of amino acids in brain microdialysates.