Capillary zone electrophoresis with diode-array detection was applied to the separation of ebrotidine and its metabolites. However, three of these, which are neutral in the conditions studied, co-migrated with the electroosmotic flow signal. Therefore, strongly overlapping peaks were observed. The main aim of this study was to show the potentiality of capillary electrophoresis in combination with chemometrics. Multivariate calibration methods were applied to quantify these analytes in synthetic mixtures. The results obtained using partial least squares (PLS) were in agreement with actual values, with an overall prediction error of 9.7%.