The effect of the granule structure on the methylation of starch was investigated by comparing the substitution patterns of potato starch methylated in granular suspension and in solution to DS 0.3. Substitution patterns were analyzed by successive digestion with α-amylase and amyloglucosidase, fractionation of the resulting malto-oligosaccharide mixture by GPC on a preparative scale, and characterization of the fractions by GLC and MALDI-MS. The mass composition of fractions with intermediate and higher degree of polymerization was indicative of enhanced clustering of substituents in granular methyl starch. On the contrary, the composition of the smaller saccharides was governed by enzyme specificity, which was also reflected in strong deviations in their monomer composition. A sequencing study on selected 'pure' small saccharides confirmed and complemented previous conclusions on enzyme specificity. © 2008 Elsevier Ltd. All rights reserved.