Effects of heating methods (hot-air heating, roasting, and microwave radiation) and kernel characteristics on the expansion of whole grains from different botanical sources have been examined. Waxy brown rice which composed of hard endosperm with tightly adhering pericarps showed explosive expansion during heating. Scanning electron microscopy showed that starch granules in hard endosperm expanded during heating, forming porous internal structure. Meanwhile those in soft endosperm remained intact since moisture vaporized into the void surrounding the granules. Whole wheat which expanded to the least extent during heating showed the formation of large fissures between pericarp and seed coat, indicating improper rigidity of pericarps as well as endosperm texture for puffing. The degree of expansion and microstructure of kernel varied depending on the heating methods applied due to their different heat transfer characteristics. Hot-air heating resulted in the higher extent of expansion than roasting or microwave radiation. Whole grains heated by either roasting or microwave radiation showed not only similar extent of expansion but also internal microstructures, although roasting process created the formation of an agglomerated mass at the domain of endosperm due to the partial gelatinization of starches.