Abstract Capillary electrophoresis coupled to laser induced fluorescence detection is one of the most sensitive techniques for chemical analysis and its applicability could be remarkably increased if spectral analysis is incorporated to it. With this view we have modified the conventional system by introducing CCD and PMT measurement simultaneously. The data obtained from PMT was processed and the peak position was determined by second derivative to trigger CCD system. With this method the electropherogram for peak identification by migration time and the spectrum corresponding to each peak were simultaneously recorded. The obtained spectra for various amino acids attached to Fluorescein Isothiocyanate (FITC) are also reported.