Phenolic compounds extracted from different citrus were determined. Calibration, extraction, elution, and introduction into the sample vial was carried out automatically by a continuous flow system (CFS) coupled to capillary electrophoresis (CE) equipment via a programmable arm. The only manual operation was the centrifugation of the sample to remove the pulp. The supernatant solutions were introduced into the CFS-CE system. A C-18 minicolumn coupled into the CFS was used to perform cleanup of the samples. The analytes were eluted from the minicolumn using methanol. Quantitative analysis was carried out by the standard addition method. The method presented allows a fast, quantitative, and reproducible determination of six main phenolic compounds in citrus samples, with precision in the range of 3.0-6.5%, expressed as relative standard deviations.