Metabolic engineering of the structure of amylopectin in rice endosperm has been performed by manipulating the activities of the major isoforms of soluble starch synthase, starch branching enzyme, and starch debranching enzymes. Our results show that each isoform distinctly affects amylopectin cluster structure and that the change leads to the synthesis of novel starches with varied physicochemical properties . This paper describes these experimental results and discusses the advantage of the molecular approach for elucidation of the starch biosynthesis system and for production of novel starches.