An analytical method for the derivatization of fatty acids to methyl esters using basic catalysis with special emphasis on the identification of the different C18:1 trans isomers was developed and validated, showing excellent accuracy, precision and linearity. This method was employed to evaluate the degradation of palm olein during the deep discontinuous frying process of potatoes and bananas over 60 hours at different temperatures, simulating most habitual food processing methods used in El Salvador. It was observed that untreated oils already showed low levels of trans fatty acids (around 0.085%) although these products were marketed as if they did not contain any trans fats. As expected, the concentration of trans fatty acids in the oil increased throughout the deep-frying process, while contents in mono- and polyunsaturated fatty acids decreased. This degradation of the oil varied depending on the temperature and the amount of water of the product being cooked.