An analytical method was developed to monitor amino acids collected by in vivo microdialysis. Microdialysate was continuously derivatized on-line by mixing 6 mM naphthalene-2,3-dicarboxyaldehyde (NDA) and 10 mM potassium cyanide with the dialysate stream in a fused silica capillary to form fluorescent products. Reaction time, determined by the flow rate and volume of reaction capillary, was 3 min. Derivatized amino acids were continuously delivered into a flow-gated interface and periodically injected onto a capillary electrophoresis unit equipped with a laser-induced fluorescence detection based on a commercial microscope. Separation was performed in the micellar electrokinetic chromatography mode using 30 mM sodium dodecyl sulfate in 15 mM phosphate buffer at pH 8.0 as the separation media. An electric field of 1.3 kV/cm was applied across a 10 cm long, 10 microm internal diameter separation capillary. These conditions allowed 17 amino acid derivatives to be resolved in less than 30 s. On-line injections could be performed at 30 s intervals for in vivo samples. Detection limits were from 10 to 30 nM for the amino acids. The method was applied to monitor the acute ethanol-induced amino acid level changes in freely moving rats. The results demonstrate the utility of the method to reveal dynamics of amino acid concentration in vivo.