The possibility of applying microwave processing to obtain food grade starch phosphates was examined. To achieve this aim the efficiency of three phosphorylating salts - monosodium phosphate, disodium phosphate and sodium tripolyphosphate, applied in both conventional and microwave processing was compared and some physico-chemical properties of food grade starch phosphates obtained using different starch species were investigated. Experimental starch samples were examined by determining their rheological properties, phosphate groups content, molecular mass distribution and crystal structure. It was found that sodium tripolyphosphate applied in both conventional and microwave processing revealed the best efficiency in potato starch phosphorylation as compared to monosodium phosphate and disodium phosphate. Microwave heating revealed the catalytic effect on the phosphate groups substitution and degradation reactions as compared to conventional processing. Starch phosphates revealed diversified susceptibility to phosphorus substitution and physico-chemical properties depending on the starch origin. These phenomena were mainly related to the crystal structure and amylose content of the investigated starches. The best functional properties revealed phosphates obtained from potato starch. The starch phosphates could also be produced using tapioca and waxy corn starches as raw material. Normal corn and wheat starches could not be recommended for phosphorylation. The application of microwave ovens for the starch phosphate production needs further investigation aiming at to decreasing the degradation phenomena.