In this study, temperature rise and non-uniformity of heating of grain with different moisture contents after microwave treatment were investigated. The temperature anomalies after microwave treatment were measured for barley and wheat at four moisture levels (12, 15, 18, and 21% wet basis) and for canola at five moisture levels (8, 12, 15, 18, and 21% wet basis). Fifty grams of grain samples were heated in a laboratory scale, continuous-type, industrial microwave dryer (2450 MHz) at five power levels (100, 200, 300, 400, and 500 W) and two exposure times (28 and 56 s). Grain samples were thermally imaged using an infrared thermal camera as soon as they came out from the microwave chamber. Average, maximum, and minimum temperatures were extracted from each thermal image and the difference between maximum and minimum temperatures (DT) was calculated. The grain type had significant effect on the surface temperatures after microwave treatment. The surface temperatures increased with microwave powers and exposure times but decreased with moisture content. The average surface temperatures after microwave treatment were between 72.5 and 117.5 C, 65.9 and 97.5 C, and 73.4 and 108.8 C for barley, canola and wheat, respectively, when the applied microwave power was 500 W. At the same power level, the maximum surface temperature was between 100.3 and 140.0 C, 77.8 and 117.7 C, and 98.3 and 130.9 C for barley, canola, and wheat, respectively. Nonuniform heating patterns were observed for all three grain types at all moisture contents, power levels, and exposure times. The DT was in the range of 7.2 to 78.9 C, 3.4 to 59.2 C, and 9.7 to 72.8 C for barley, canola, and wheat, respectively. The location of hot and cold spots may vary in different dryers based on the position of magnetron and other components, but almost similar non-uniform heating pattern is expected in all microwave dryers. Therefore, this non-uniformity must be taken into consideration while developing microwave processing systems for grains.