The effects of microwaves on physicochemical properties of corn and oat starches were investigated. Separate suspensions of corn and oat starches in distilled water (8% w/w) were made and heated in a microwave oven at frequency of 2450 MHz and power of 360 W for 2.5, 5, 7.5 and 10 min. Then, swelling power, solubility, relative viscosity (using U-tube viscometer), cold water viscosity (using Rapid Visco Analyser) and textural properties (using Texture Profile Analyser) were investigated. Results showed that as the time of microwave processing increased, cold water viscosity and gel hardness decreased, however, swelling power and water solubility increased. Comparing to the conventional heating method, more reduction in the relative viscosity was observed for the microwave processed samples. In general, results showed that microwave processing had a stonger effects on structural and molecular properties of corn and oat starches than the conventional cooking. These changes may be further affect the quality of the final products.