Starch is synthesized in semi-crystalline granular structures. Starches of different botanical origins possess different granular sizes, morphology, polymorphism and enzyme digestibility. These characteristics are related to the chemical structures of the amylopectin and amylose and how they are arranged in the starch granule. In this paper, structures and locations of amylose and amylopectin molecules in the granule are reviewed. The branch structures of amylopectin molecules and their relationship with the polymorphism, structures, and morphology of the starch granules are discussed. Internal structures of starch granules revealed by confocal laser-scattering microscopy and by using a surface-gelatinization method are compared and their effects on surface pinholes and serpentine channels of the starch granules are discussed.