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Microwave heating is believed to be a more uniform type of heating compared to conventional methods of heating. Temperature distribution studies, however, have shown that temperature is not uniform throughout the samples during microwave heating. An infra-red thermal camera was used in this study to determine the temperature distribution in bulk rye and oats at 14, 16, and 18% moisture content after being exposed to microwaves in a pilot-scale industrial microwave drier. Fifty grams of grain were placed in the sample holder and allowed to pass on a conveyor belt under the applicator at 0, 200, 300, 400, and 500 W for 28 or 56 s. There were hot and cool regions in the samples. The average temperature of the 14% MC rye after 28 s exposure times for 0, 200, 300, 400, and 500 W were 27.6, 49.2, 65.1, 59.0, and 85.4oC, respectively and the average temperature of 14% MC oats at the same conditions were 27.2, 33.1, 35.5, 46.6, and 51.4oC, respectively. The temperature difference between hot and cool regions in a given sample varied between 23 to 62oC for rye and 7 to 25oC for oats. The preliminary results of this study suggest that while using microwave as a heat treatment for grains, the maximum temperature should be taken into consideration, when developing microwave processing systems for grains.