The percentage (%) fatty alcohol and fatty acid compositions of the wax esters of large numbers of Stage V and females of Calanus hyperboreus, C. glacialis and C. finmarchicus taken in late August to late September from Arctic waters (Kongsfjord in Svalbard, 78°57’ N, 11°50’ E) are presented. The data reveal that these stages of development of the 3 species can be discriminated on the basis of the % of 22:1n-11 fatty alcohol in their large levels of wax esters, with C. hyperboreus having the highest % followed by C. finmarchicus and then C. glacialis. Equally, C. hyperboreus has the lowest % of 20:1n-9 fatty alcohol in its wax esters with C. finmarchicus having a higher % and C. glacialis the highest %. Relatively minor differences occur in the fatty acid compositions of the wax esters of the 3 species, which consisted principally of 20:1n-9 (15 to 18%) and 22:1n-11 (10 to 15%), together with the diatom-derived fatty acids 16:1n-7 (20 to 23%) and 20:5n-3 (11 to 13%). The flagellate-derived fatty acids, 18:4n-3 (3 to 6%) and 22:6n-3 (1 to 3%), were minor constituents. The fatty acid compositions of the small amounts of polar lipid in the 3 species were indistinguishable with 22:6n-3 (41 to 46%) and 20:5n-3 (22 to 24%) being the major components. We conclude that Stage V and females of the species can be distinguished in autumn on the basis of the different % of 22:1n-11 and 20:1n-9 fatty alcohols in their wax esters and that de novo lipid biosynthetic activity in the copepods increases in the order C. finmarchicus < C. glacialis < C. hyperboreus. We discuss the results in terms of the contributions of fatty acids and fatty alcohols biosynthesised de novo and fatty acids derived from the diet to the copepods’ lipids, the role of 20:1 and 22:1 fatty alcohols and fatty acids as energy sources, and the possible role of 22:6n-3 in the copepods’ physiology.