Two different methods for determining the levels of glycidol fatty acid esters (GEs) in edible oil-the German official indirect method and the direct LC-MS method—are compared. In some cases, the indirect method showed lower GE levels than the direct method. This was investigated using model studies, which revealed two possible causative factors during the acid treatment of the indirect method: (1) incomplete elimination of GE in oil that was high in GEs initially and (2) generation of GEs and/or its relevant compounds in oil that was rich in partial acylglycerol. Both these factors contributed to the subsequent underestimation of GE levels. The above technical limitations of the indirect method found in the present study has led to the inference that the direct method can more precisely determine the GE levels for a wider range of fats and oil products than the indirect method.