An experimental investigation ascertained the variation of the contents of saturated, unsaturated and polyenoic fatty acids, as well as of the trans-isomers of unsaturated fatty acids, in different vegetable oils (virgin olive oil, refined sunflower, refined peanut) submitted to either conventional or microwave heating. The results obtained showed that heat treatment causes a worsening of the nutritional quality of the fatty fraction. As a consequence, the contents of unsaturated and polyenoic fatty acids decreased, with greater variations in the oils heated by microwave than by a conventional oven, while the saturated fatty acid contents did not change substantially. The heat treatments also caused an increase in the trans-isomers of unsaturated fatty acids and this was more evident after microwave treatment.