Micellar electrokinetic chromatography allows the efficient separation of biogenic amines and amino acids in biological samples. Analytes of interest, sample composition, and sample matrix may vary between studies, which necessitates optimization of separations to meet the requirements and conditions of an experiment. Factorial analysis is an efficient tool to accomplish this type of optimization involving multiple interacting factors. The present study describes an optimization procedure for separation of the inhibitory neurotransmitter GABA utilizing capillary electrophoresis with laser induced fluorescence detection. Standards labeled with the flourogenic reagent 3-(2-furoyl)quinoline-2 carboxaldehyde were separated with varying concentrations of borate buffer, beta-cyclodextrin, sodium dodecyl sulfate and pH. The optimized separation method had a correlation coefficient between concentration of GABA and fluorescent signal of 0.98, and was linear in the desired concentration range of 25 nM-10 microM. Glutamic acid, aspartic acid and taurine were also quantified using this separation. When applied to microdialysate collected from the region of the suprachiasmatic nucleus, this separation was able to measure daily variations in GABA levels. The factorial design experiment has proven to be a useful tool, allowing adjustments in the separation of neurotransmitters based on individual requirements.