Sixteen free amino acids were separated by capillary electrophoresis (CE) using zwitterionic buffers of pH 9.8 and detected amperometrically using a copper microelectrode. Low conductivity buffers make possible the use of higher buffer concentrations. This depresses the electroosmotic flow, leading to a better separation of the amino acids compared to that obtained using strong electrolytes. The use of zwitterionic buffers also minimizes the amount of Joule heating in the capillary leading to more efficient separations. Perhaps most importantly for electrochemical (EC) detection, these buffers reduce the noise due to high separation current at the EC detector. The increased signal-to-noise ratio (S/N) results in much better detection limits for amino acids than those reported previously for capillary electrophoresis/electrochemistry (CEEC) with a copper electrode. Detection limits ranged from 10 to 400 nM, and the response was linear over three orders of magnitude for most of the amino acids. The system demonstrated good long-term stability and reproducibility with a relative standard deviation (RSD) of less than 5% for both the migration time and peak current (n = 20). This method was employed for the determination of amino acids in urine and in brain microdialysate samples.