An in-channel configuration for amperometric detection has been adopted in capillary electrophoresis performed in photolithographically microfabricated chips. This electrode alignment, compared with the more conventional end-channel configuration, led to a better peak resolution and a higher sensitivity, because it involves no gap between the channel outlet and the working electrode, thus preventing the dispersion of the analyte band leaving the separation channel into the comparatively large detection reservoir. All details concerning the chip fabrication, as well as injection and detection procedures adopted are carefully described. The performance of this approach was first optimized for the experimental parameters affecting both separation and detection steps and then assayed for the separation of two synthetic food dyes, Green S and Patent Blue, concomitantly present in synthetic samples. Under the optimized conditions thus recognized (background electrolyte: 40mM aqueous carbonate–bicarbonate buffer at pH=10.5, separation voltage: 1300V, amperometric detection at controlled potential of 0.9V vs. Ag / AgCl, Cl ( sat ) - ), a well satisfactory resolution could be achieved within less than 300s. The recorded peaks were characterized by both a good repeatability (7%) and a linear dependence of their height over a wide concentration range (about 2 orders of magnitude). The detection limit, estimated for a signal-to-noise ratio of three was 10μM for Patent Blue and 17μM for Green S. The application of the method to some commercial soft-drinks and candies is also presented.