Microstructural changes of potato and corn starch aqueous solutions associated with their gelatinization and retrogradation processes were examined through the use of small- and wide-angle X-ray scattering. It was found that the structural changes during these two processes were dominantly affected by the amount of phospholipids and phosphates contained in the starch. The phosphates contained in the amylopectin of the starch granule allow easy penetration of water into the structure, thus causing easy swelling or high solubility. This simultaneously allows greater freedom of chains, thus causing the recrystallization of the chains during the retrogradation process. On the other hand, in corn starch, which contains a lower amount of phosphates and a complex structure formed between phospholipid and amylose, the chain movements are much reduced, resulting in a higher gelatinization temperature and a reduction of recrystallization during retrogradation and a broad distribution of crystal size. In both starches, a micro-phase separated inhomogeneous structure was suggested in the amorphous state above the gelatinization temperature, which appears to be associated with the presence of highly branched amylopectin units.