This paper describes the in-column derivatization, stacking, and separation of amino acids by CE in conjunction with light-emitting diode-induced fluorescence using naphthalene-2,3-dicarboxaldehyde (NDA). According to the relative electrophoretic mobilities and the migration direction in tetraborate solution (pH 9.3), the injection order is cyanide, then amino acids, then NDA. Once poly(ethylene oxide) (PEO) migrates through the capillary under EOF, the amino acid.NDA derivatives, amino acids, and CN- ions migrating against the EOF enter the PEO zone. As a result of increases in viscosity and possible interactions with PEO molecules, the reagents/analytes slow down such that they become stacked at the boundary. In comparison with the off-column approach to the analysis of amino acids, our proposed method provides a lower degree of interference from polymeric NDA compounds and other side products. As a result, the plot of the peak height as a function of gamma-aminobutyric acid (GABA) concentration is linear over the range from 10(-5) to 10(-8) M, with the LOD being 4 nM. We demonstrate the diagnostic potential of this approach for the determination of amino acids, including GABA and glutamine, in biological samples through the analysis of large volumes of cerebral spinal fluids without the need for sample pretreatment.