The aim of this study was to evaluate the effect of dietary lipid classes (phospholipid vs. neutral lipid) and level of n-3 highly unsaturated fatty acids (HUFAs) on growth, survival and digestive enzymatic activity in Atlantic cod (Gadus morhua) larvae. Larvae were fed enriched rotifers from mouth opening and were weaned to formulated diets during a co-feeding period lasting from 17 days post hatch (dph) to 24 dph. Larvae were fed exclusively compound diets from 24 dph until the end of the experiment. Three isoproteic and isolipidic compound diets with gradually decreasing levels of DHA and EPA in the dietary phospholipid fraction (diet PL3NPL1NNL1) and increasing levels of total dietary neutral lipids (PL3bPL1bNL1) were used. Larvae fed the PL3 or PL1 had a significant higher dry weight than larvae fed the NL1 diet at the end of the experiment (45 dph). Survival did not differ significantly between treatments. A gut maturation index based on the relation between the amount of the brush border enzyme alkaline phosphatase and the cytosolic enzyme leucine-alanine aminopeptidase showed that the enterocyte maturation on 35 and 45 dph was better in larvae fed the PL3 and PL1 diet than larvae fed the NL1 diet. Dietary composition did not significantly affect the activity of α-amylase, but an age specific decrease in activity was observed. The dietary composition did affect the specific activity of trypsin, although showing variation in pattern between different larval ages at sampling. The activity of neutral lipase showed high variability between dietary treatments, but at the end of the experiment the specific activity of neutral lipase was positively connected to the dietary neutral lipid levels. The results from this study showed that cod larvae use DHA and EPA in the phospholipid fraction more efficiently compared to those in the neutral lipid fraction