A nanocapillary array was integrated into a microfluidic device and its ability to concentrate analytes was characterized. Through the application of an electric field across the channel, large molecules were concentrated in front of the nanocapillary array, and a concentrated analyte band was ejected from the channel by reversing the polarity of the electric field. The effects of nanocapillary diameter, analyte charge, analyte concentration, analyte plug length, and analyte relative mobility were investigated. Concentration factors up to 300-fold were measured for fluorescein. By concentrating anionic FITC-labeled peptides, it was demonstrated that the magnitude of the electrophoretic mobility did not have a measurable effect on the concentration factor. Therefore, multiple analytes can be concentrated in front of the same nanocapillary array without adjusting the conditions, provided the analytes have the same net charge. In the presence of an electric field, a charge trapping effect was observed; small anionic molecules can be concentrated in front of nanocapillary array with channel diameters which are orders of magnitude above the molecular weight cut-offs for hydrodynamically driven systems. The concentrating process was found to be very efficient for fluorescein, as no leakage through the nanocapillary array or sorption of fluorescein to the nanocapillary array was observed. Due to their flexibility and efficiency, it is anticipated that nanocapillary arrays will find increased utility in electrokinetically driven microfluidic systems.