The analysis of partially methylesterified oligogalacturonides plays a key role both in the elucidation of the fine structure of the polysaccharide pectin and in the study of pectin-acting enzymes. Experimental methods performing the separation, detection and quantification of oligogalacturonides are, therefore, of crucial importance in the drive to understand structure-function relationships in pectin containing systems, both in vitro and in vivo. In this work standard samples of unesterified and partially methylesterifed galacturonides, and enzymatic digests of several pectin samples possessing distinct intramolecular patterns of methylesterification were studied using capillary electrophoresis (CE) and polysaccharide analysis using carbohydrate gel electrophoresis (PACE). In addition to yielding interesting information regarding the fine structures of the different pectic substrates digested, the study has been used as a vehicle in order to compare the two recently reported methods.