Biodiesel is one of the most promising renewable liquid fuels. It can be obtained from any raw material containing fatty acids, however the main industrial process today remains based on vegetable oil transesterification with methanol. In recent years also interesterification of oils with methyl acetate as reactant had been studied. Interesterification of triglycerides with methyl acetate provides a promising alternative of transesterification because triacetin is formed instead of glycerol. Both processes are realized in presence of homogeneous alkoxide catalysts dissolved in conjugate alcohol, for example potassium methoxide in methanol, potassium ethoxide in ethanol, potassium isopropoxide in isopropanol etc. If the catalytic system contains alcohol, simultaneously to oil interesterification with methyl acetate the transesterification reaction of oil with alcohol from catalytic system can proceed. Thereby the intricate mixture of fatty acid alkyl esters (FAAE) can be produced and it is not clear how successfully the often used European standard method EN14103 or its modification can be employed for the analysis of such mixtures. In order to elaborate an effective and simple method, in this work GC was used for analysis of the mixtures of fatty acid methyl (FAME) and isopropyl (FAiPE) esters. Pure FAME and FAiPE were obtained by its synthesis from rapeseed oil with following vacuum-distillation. Determination of their composition has been made by employing the certified reference material for FAME and new internal standard ethyl laurate. Different response factors for each type of esters have been determined and used for the more correct analysis of FAAE compositions.