Thermostable branching enzyme (BE, EC 2.4.1.18) from Rhodothermus obamensis in combination with amylomaltase (AM, EC 2.4.1.25) from Thermus thermophilus was used to modify starch structure exploring potentials to extensively increase the number of branch points in starch. Amylose is an important constituent in starch and the effect of amylose on enzyme catalysis was investigated using amylose-only barley starch (AO) and waxy maize starch (WX) in well-defined ratios. All products were analysed for amylopectin chain length distribution, alpha-1,6 glucosidic linkages content, molar mass distribution and digestibility by using rat intestinal ci-glucosidases. For each enzyme treatment series, increased AO content resulted in a higher rate of alpha-1,6 glucosidic linkage formation but as an effect of the very low initial branching of the AO, the final content of alpha-1,6 glucosidic linkages was slightly lower as compared to the high amylopectin substrates. However, an increase specifically in short chains was produced at high AO levels. The molar mass distribution for the enzyme treated samples was lower as compared with substrate WX and AO, indicating the presence of hydrolytic activity as well as cyclisation of the substrate. For all samples, increased amylose substrate showed decreased alpha- and beta-amylolysis. Surprisingly, hydrolysis with rat intestinal ci-glucosidases was higher with increasing ci-1,6 glucosidic linkage content and decreasing Mw indicating that steric hindrance towards the alpha-glucosidases was directed by the molar mass rather that the branching density of the glucan per se. Our data demonstrate that a higher amylose content in the substrate starch efficiently produces alpha-1,6 glucosidic linkages and that the present of amylose generates a higher Mw and more resistant product than amylopectin. The combination of BE AM BE provided somewhat more resistant alpha-glucan products as compared to BE alone.