Heat treatment is used to physically modify starch to meet requirements for certain food products such as canned food, bread or noodles. In oats, the application of heat is used to inhibit activities of enzymes that cause undesirable effects on the end-product quality. However, it may also affect starch structure and functional properties of oats. This study examined the effects of heat treatment processing on starch molecular structure and physicochemical properties of oats using eight oat genotypes grown at four sites in Australia. Compared to non-heat-treated oats, heat treatment resulted in shorter amylopectin chains, higher amounts of long amylose chains and higher amylose content where amylose content and the relative amounts of long and short amylose chains are important determinants of functional properties of cereal-based food products. Heat treatment also increased gelatinization and pasting temperature but decreased gelatinization enthalpy, breakdown viscosity, final viscosity and setback viscosity. The peak viscosity remained unchanged. The results of this study show how heat-treated oats changes starch structure and properties, which could impact on processing for specific food products.