Abstract Omega-6 fatty acids are essential polyunsaturated fatty acids (PUFAs) and found in refined vegetable oils, nuts and seed that play a very important role in heart and brain function, along with normal growth and development. These acids have at least two double bonds and 18 carbon atoms (18:2) that the number of double bonds present refers to the degree of unsaturation of a fatty acid. A first phase of calculations was performed using PM3 semi-empirical method to characterize to potential energy surface of omega-6 fatty acids: Linoleic (18:2), γ-linolenic (18:3), Eicosadienoic (20:2), Dihomo-γ-linolenic (20:3), Arachidonic (20:4), Docosadienoic (22:2), Adrenic (22:4), Docosapentaenoic (22:5), Tetracosatetraenoic (24:4) and Tetracosapentaenoic (24:5). Afterwards, the lowest energy conformer of each acid was selected for the geometric optimization step and PM3 geometries were fully optimized using the DFT method at the B3LYP/6–311++G (d,p). The optimized structural parameters were used in the vibrational frequency calculations at the DFT level to characterize all stationary points as minima. The effect of a fatty acid structure on its molecular properties were analysed.