Capillary zone electrophoresis (CZE) was employed to determine the correlations between migration time and degree of esterification (DE) of pectinesterase-de-esterified pectins (PDPs) and alkaline-de-esterified pectins (ADPs) using 50 mM phosphate buffer (pH 6.5) as carrier electrolyte solution and 15 KV as applied voltage. Results showed that pectins with higher DEs exhibited shorter migration times. Linear correlation (r = 0.995) between migration time and DE of ADPs was observed, whereas down-curve correlation in PDPs was observed, regardless of the capillary length used (effective length, 30 and 60 cm). In addition, PDP appeared to migrate faster than ADP with the same DE under the same experimental conditions.