An acridinium ester has been used to tag mixtures of peptides followed by separation by capillary electrophoresis with chemiluminescence detection. The labelling of the peptides was performed at the picomole level. The chemiluminescence reaction conditions were optimized for the acridinium tag resulting in CE separations performed on attomole amounts of tagged peptides. Baseline resolution was obtained for a separation of standard peptides. The detection sensitivity was found to improve when multiple acridinium labels were attached to the peptides. The effect of acridinium tagging on the migration rate of the peptides was also studied. The increased weight of the acridinium tagged analyte increased the run time and resolution of a separated tryptic digest without resulting in excessive band broadening.