A capillary zone electrophoresis (CZE) method for the simultaneous determination of 20 polyphenols in wine was developed. The separation was performed using fused-silica capillaries of 75 μm i.d. and a 30 mM sodium tretraborate buffer solution at pH 9.2 with 5% isopropanol as a background electrolyte. A capillary voltage of +25 kV with pressure-assisted (3.5 kPa) separation from minute 18 was applied, thus achieving a total analysis time of <25 min. Instrumental quality parameters such as limits of detection (LOD, values between 0.3 and 2.6 mg/L), linearity (r(2) > 0.990), and run-to-run and day-to-day precisions (RSD values lower than 6.5 and 15.7%, respectively) were established. Three different calibration procedures were evaluated for polyphenol quantitation in wines: external calibration using standards prepared in Milli-Q water, standard addition, and pseudomatrix-matched calibration using wine as a matrix. For a 95% confidence level, no statistical differences were observed, in general, between the three calibration methods (p values between 0.11 and 0.84), whereas for some specific polyphenols, such as cinnamic acid, syringic acid, and gallic acid, results were not comparable when external calibration was used. The CZE method using pseudomatrix-matched calibration was then proposed and applied to the analysis of polyphenols in 49 Spanish wines, showing satisfactory results and a wide compositional variation between wines. Electrophoretic profiles and other compositional data (e.g., peak areas of selected peaks) were considered as fingerprints of wines to be used for characterization and classification purposes. The corresponding data were analyzed by principal component analysis (PCA) to extract information on the most significant features contributing to wine discrimination according to their origins. Results showed that a reasonable distribution of wines depending on the elaboration areas was found, tyrosol and gallic, protocatechuic, p-coumaric, and caffeic acids being some representative discriminant compounds.