Regular starches contain two principal types of glucan polymers: amylopectin and amylose. The structure of amylopectin is characterized according to the unit chain length profile and the nature of the branching pattern, which determine the alignment of glucan chains during biosynthesis. The organization of glucan chains in amylopectin and their impact on the structure of starch are still open to debate. The location of amylose and its exact contribution to the assembly of crystalline lamellae in regular and high-amylose starch granules also remain unknown. The primary focus of this thesis is the organization and flexibility of glucan chains in crystalline lamellae. The organization and flexibility of glucan chains in native, annealed (ANN), and heat-moisture treated (HMT) normal, waxy, hylon V, hylon VII, and hylon VIII corn starches were examined. This study has shown for the first time that increased amounts of apparent amylose in B-type starches hinder the polymorphic transition (from B to A+B) during HMT. The research has also demonstrated that an iodine-glucan complex transformed the B-type polymorphic pattern of hylon starches into a V-type pattern. The differential scanning calorimetry (DSC) results showed that ANN- and HMT-induced changes were most pronounced in hylon starches. These findings suggest that the glucan tie chains influences the assembly of crystalline lamellae in high-amylose starches. The relationship between the internal unit chain composition of amylopectin, and the thermal properties and annealing of starches from four different structural types of amylopectin was investigated by DSC. The onset gelatinization temperature (To) correlated negatively with the number of building blocks in clusters (NBbl) and positively with the inter-block chain length (IB-CL). The enthalpy of gelatinization (∆H) correlated positively with the external chain length of amylopectin. Annealing results showed that starches with a short IB-CL were most susceptible to ANN, as evidenced by a greater increase in the To and Tm. The increase in enthalpy was greater in starches with long external chains and IB-CLs. These data suggest that the internal organization of glucan chains in amylopectin determines the alignment of chains within the crystalline lamellae and thereby the thermal properties and annealing of the starch granules.