In this article, we present a simple and cost-effective method for the determination of amino acids in cerebrospinal fluids (CSF) by using capillary electrophoresis-light-emitting diode-induced fluorescence detection. When using a deactivated capillary filled with 0.6% poly(ethylene oxide) (PEO, M r 6.0 × 10 5) prepared in 10 mM tetraborate (pH 9.3), we have achieved the limits of detection (S/N = 3) in the range of 10–30 nM for naphthalene-2,3-dicarboxaldehyde (NDA) derivatized amino acids (detected in the anodic side) in the absence of electroosmotic flow (EOF). In order to further improve sensitivity, stacking and separation of CSF samples in the presence of EOF has been applied. When high voltage is applied, the analytes migrating against EOF slow down and are stacked at the boundary between 2.0% PEO (M r 8.0 × 10 6) prepared in 10 mM tetraborate (pH 9.3) and sample zone. The stacking approach provides the LODs at the nM level for the analytes (detected in the cathodic side) when injecting at 30 cm height for 150 s. The two proposed methods provide comparable results for the determinations of glycine (Gly), glutamine (Gln), and glutamate (Glu) in CSF samples from patients suffered from inflammation, epilepsy, and jaundice without sample preparation, but the stacking method is more sensitive and allows for the determination of -aminobutyric acid (GABA).