Moisture content of normal, waxy, and high amylose com starches was adjusted to 10-35%, and irradiated in a microwave oven. The effect of microwave irradiation on the crystalline structure of starch was measured by using a differential scanning calorimetry (DSC), and X-ray diffractometry. Pasting viscosity profile was also determined by using a rapid viscoanalyzer (RVA). For all the 3 types of starches tested, the rate of temperature increase by the microwave irradiation was faster and more rapidly reached the maximum temperature of the pressure bomb ($120^{circ}C$) when the moisture content was higher. X-ray diffraction and DSC data revealed that the microwave irradiated starch underwent partial disruption of crystalline structure. RVA studies showed that the irradiation caused significant reductions in maximal viscosity and breakdown, whereas pasting temperature was increased. Overall trends revealed that the microwave irradiation on the starch containing limited moisture content (less than 35%) provided the effects similar to the heat moisture treatment. These effects became more significant when the moisture content was higher. Compared to waxy com starch, normal, and high amylose com starches appeared to be more susceptible to the microwave irradiation.