Proteome analysis was used to study the effects of feeding early Atlantic cod (Gadus morhua) larvae with a saithe (Pollachius virens) protein hydrolysate (SPH). Protein hydrolysates have previously been shown to beneficially affect fish larval development. Feeding was initiated on day 2 post hatch (ph) or as soon as the larvae opened their mouth and the protein expression was monitored 4 days later or in 6-dph cod larvae. The results demonstrated changes in the abundance of 13 protein spots in the cod larvae fed SPH. Of these, seven protein spots were up-regulated and six protein spots showed down-regulation. Five of the up-regulated proteins in cod larvae are known to be involved in energy metabolism. A few early larval specific proteins were down-regulated in the SPH-fed cod larvae possibly because of an enhanced development in this group relative to the control group. Two trypsin isoforms were detected within the cod larval proteome. The detection of the trypsin spots was made possible by co-electrophoresis of known cod trypsins with the cod larval protein extract. Surprisingly, no difference in trypsin content was observed between the SPH-fed and the control larval groups.