Glycogen branching enzymes (GBEs) from Escherichia coli (EcBE), Deinococcus geothermalis (DgBE) and Vibrio vulnificus (VvBE) have different characteristics for branching activities, especially in chain-length transferred. In this study, the three GBEs were used to produce cluster-starches from amylopectin, and physicochemical properties of the cluster-starches were intensively analyzed in relation to their molecular structures. Side chain distribution of these cluster-starches obviously shifted to short and medium chains that made a significant decrease in their molecular weight and size. They thereby increased water-solubility without exhibiting viscosity. There was no retrogradation of DgBE- and VvBE-clusters during storage at 4℃ for 17 days. Catalytic efficiency of porcine pancreatic α-amylase (PPA) was lowest for VvBE-cluster. In conditions mimicking the human intestine, EcBE, DgBE and VvBE cluster-starches were digested 100%, 67.1% and 73.0%, respectively, in comparison with that of amylopectin. Consequently, the modified clusters from amylopectin produced by DgBE and especially VvBE may be new functional materials for food and pharmaceutical industries.