A new and rapid microwave assisted derivatization method for the determination of fatty acids in edible oil by GC MS was developed. The optimum conditions for derivatization, such as the derivatization solvent composition, microwave assisted derivatization pressure and time were studied for KOH methanol and H 2SO 4 methanol systems. The experimental results were compared with those obtained by traditional method of normal temperature derivatization .The applied range of the two derivatization systems was also discussed in detail. The derivatization was accomplished in 1 minute. Heptane was used as extraction solvent. The method is rapid, efficient, accurate and solvent saving.