The aim of the present study was to compare effects of dietary n-3 highly unsaturated fatty acids (HUFA) being incorporated in the phospholipid (PL) or in the neutral lipid (NL) fraction of the larval feed, on larval growth and histology of digestive organs in Atlantic cod (Gadus morhua L.) larvae. Three isoproteic and isolipidic diets, labelled according to the percentage of n-3 docosahexaenoic acid and eicosapentaenoic acid contained in NL1 or in PL1 and PL3 of the diets, were fed to cod larvae from 17 days post hatching (dph) to 45 dph. In the liver, hepatocytes and their nuclei were smaller in NL1 larvae compared with the PL larvae; the mitochondrial membrane structures were less dense and the amount of lipids observed in the liver was significantly higher in NL1 larvae compared with the PL3 larvae. The liver and gut size was related to larval size, with no differences between the larval groups. The results demonstrated that the essential fatty acids were more beneficial for cod larvae when they were incorporated in the dietary polar PL rather than in the NL, and that the n-3 HUFA requirements in cod larvae is possibly higher than that in the PL1 diet.