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The effect of microwave heating on the Fatty Acid Profiles (FAPs) of three Nigerian Vegetable oils (soya, groundnut and palm oils) was studied. Samples of the oils were separately heated for thirty minutes in a microwave oven. FAP of each oil was analyzed before and after microwave heating using gas chromatograph. Comparative study of the FAPs of the three oils before and after microwave heating showed that the microwave heating had a very marginal impact on the compositions of their fatty acids. Very slight quantitative changes were observed on the composition of the fatty acids, the proportion of Unsaturated fatty acid (USFA) and Saturated fatty Acid (SFA) in the three oil samples as a result of the microwave heating.