The objective of the studies was to compare the changes in physicochemical parameters (peroxide, acid, iodine, anisidine values, Totox index, polar compound content, density) and fatty acids composition in refined rapeseed and sunflower oils, occurring during various heating methods, microwave and conventional. Based on the studies carried out it was found that more adverse changes occurred in microwave heated oils. This method of heating causes greater increase in anisidine value, Totox index, acid value and polar compound content. Totox index attained the highest values in microwave heated oils, namely, 157 for rapeseed oil and 184 for sunflower oil. Significantly lower values were noted for oils that were conventionally heated, namely, 60-85 for rapeseed oil and 96-108 for sunflower oil. For the remaining indices there was no unequivocal effect of the heating method on the changes in the values of these parameters. The unsaturated fatty acid content decreased as a result of heating the oils, which is proven by the drop in iodine value and by changes in fatty acids content. In the studied oils a small drop in the value of ΣUFA/ΣSFA ratio was observed regardless of the heating method.