High-density (HD) rotifer culture systems have been recently commercialized, but are not commonly used by the aquaculture industry. The aim of this study was to determine if HD systems could be used in cod hatcheries. An enrichment strategy using the commercial products, ArteMac and Protein Selco Plus (Com), was compared with the manufacturer's suggested enrichment, using Pavlova-DHA (Pav). The Pav enrichment increased the eicosapentaenoic acid (EPA) levels in rotifers, but reduced the docosahexaenoic acid (DHA) and 22:5n-6 (n-6DPA, docosapentaenoic acid) levels. Larvae EPA levels in both polar and neutral lipids were relatively stable in the larvae fed with Com-rotifers; while they were higher in early stages, they were progressively reduced through ontogeny in the Pav-rotifers fed-larvae. DHA levels in polar lipids decreased in larvae, particularly when fed with HD-Pav rotifers. In all larvae, arachidonic acid (ARA) levels increased in the polar and neutral lipids, regardless of treatments. In both lipid fractions, the levels of ARA were quite stable in time, but still higher in larvae fed with Com-rotifers. Bacterial load was lower in larvae fed with Pav-rotifers. Denaturing gradient gel electrophoresis (DGGE) bacterial profiles of larvae and rotifers were all similar. This study shows the potential of using HD systems to produce rotifers, but highlights the necessity of adjusting the nutritional composition of rotifers prior to being fed to larvae.