Abstract Three industrial high methoxyl pectins have been fractionated by size exclusion chromatography (SEC) on a preparative scale and the chemical composition, viscosity and light scattering behaviour of the fractions have been investigated. Chemical analysis revealed that the composition varies greatly from one SEC fraction to another. In all three pectin samples, the fractions of low molecular size contain most of the free neutral polysaccharides as well as some free pectin ‘hairy regions’. In addition, the lemon pectin samples contain some pectin molecules of large size which are rich in neutral sugars. Phenolic and proteinaceous compounds coelute with neutral sugar-rich fractions. However, in the apple pectin, phenolics and proteins occur predominantly in the fractions of low molecular size. Lemon pectin molecules, especially that of the lemon A sample, are prone to aggregation in the presence of calcium cations. The aggregate fraction can be disrupted by shear forces, heating or the presence of a chelating agent. The formation of such calcium-pectinate aggregates seems to be due to the presence of some molecules with low degrees of methoxylation. Light scattering measurements also suggest that even very narrow SEC fractions remain highly heterogeneous on the basis of their molecular weight, thus indicating large differences in molecular conformation.