Capillary electrochromatography (CEC) is a technique that uses electroosmotic flow for the propulsion of the mobile phase in liquid chromatography. Employing packed fused-silica capillaries, fluorescence detection is possible in a packed section of the separation capillary (in-column detection) or in an emptied section (on-column detection). These two detection modes were compared with each other with respect to detection limit, precision and instrumental band-broadening effects. By monitoring plug-like solute zones it is shown that with in-column detection the signal noise is dependent on the signal height, whereas with on-column detection the signal noise is independent of the signal height.