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In this study, the influence of microwave irradiation on some physico-chemical properties and several pharmaceutical technological parameters of potato and maize starches was investigated. Changes in their habits were observed and decrease in moisture contents caused by the electromagnetic irradiation was determined. The crystalline structures and the micromorphological parameters of the starches were affected by microwave irradiation in different ways depending on the botanical origin of the samples. The tensile strengths of the compacts containing starches were decreased, their wetting properties were enhanced by the thermal process applied. Furthermore, microwave irradiation reduced the surface free energy and the polarity of the compacts significantly. Samples treated by conventional heating were used to compare the effects of microwave irradiation on the examined properties and parameters of these starches.