Triglyceride composition and trans fatty acid content of corn oil subjected to microwave and conventional heating were evaluated with the aid of central composite design methodology. Oil samples with and without α-tocopherol were prepared on the basis of central composite design and, the effects of the main three factors (temperature, contact time, and the amount of α-tocopherol) were tired to investigate 10 at different five levels. Linoleic acid-linoleic acid-linoleic acid content in triglyceride structure of corn oil and the amount of trans fatty acids in the same oils were taken as response values for evaluation of central composite design assays. Based on the response surface, the optimum conditions (at which trans fatty acid formation and the change in the triglyceride composition are minimum) were determined for both heating procedures. The results showed that the increasing of the temperature and contact time increased the trans fatty acid formation and changed triglyceride structure of the oil in both heating techniques, although, the addition of α-tocopherol at high concentration caused pro-oxidant effect on triglyceride composition (bad effect), while reducing the formation of trans fatty acid (good effect). The results revealed that the heating 20 treatments caused significant changes in the triglyceride composition and trans fatty acid isomers of unsaturated fatty acids of the oil, while the saturated fatty acid contents did not change substantially. These alterations were much greater in microwave-heated samples (trans fatty acid ≤ 7.26%) than in Q3 corresponding samples heated in a conventional stove (trans fatty acid ≤ 0.56%).