Pectins differing in their degree and pattern of methylesterification are important in diverse aspects of plant physiology and also in many industrial applications. Determination of methylesterification fine structure and knowledge of enzyme specificities in modification and fragmentation of pectin are key to understanding the relationship between structure and function. The development of methodologies for the detection, separation and sequencing of different partially methylesterified oligogalacturonides (Me-OGAs) is consequently very important. Polysaccharide analysis using carbohydrate gel electrophoresis (PACE) has been shown to be powerful for the quantitative resolution of species different in degree of polymerization (DP) and/or degree of methylesterification (DM). Mass spectrometry (MS) has, to date, been the only tool with which to obtain isomeric information. However, it is not quantitative, and the presence of isobaric species makes the interpretation of the fragmentation patterns complicated. Here, we present evidence that Me-OGAs with the same DP and DM but different patterns of methylesterification (structural isomers) can easily be separated and quantified using PACE.