Abstract The chromatographic behavior of molecular species of free fatty acids, triglycerides, sterol esters and wax esters on Chromarods‐SII was investigated in four developing solvent systems of different polarities. In accordance with previous reports it was observed that molecular species within a lipid class are partially separated according to the chain length and degree of unsaturation of the acyl groups. The separation is more affected by the degree of unsaturation than the chain length, especially in nonpolar solvent systems. In polar solvent systems the separation within a lipid class is less efficient; a slight separation according to the chain length was observed, and the degree of unsaturation had little or no influence. The partial separation of molecular species within a class leads to the superimposing of certain lipid classes, for example glyceryl ethers and highly unsaturated fatty acids of marine origin. This poses a potential problem in identification of Iatroscan peaks. However, with totally hydrogenated marine lipid samples a complete separation of the lipid classes was achieved when developed in a nonpolar solvent system. It is proposed that at least two kinds of authentic standards varying in the degree of unsaturation and chain length should be used for the identification of the peaks of natural lipid samples of unknown composition, and that total hydrogenation be applied to improve separations and ensure sample stability, and probably to improve quantitation accuracy.