The aim of this project was to investigate trypsins in early Atlantic cod larvae (Gadus morhua) as these enzymes are known to play a key role in the digestive function at that stage. Activity measurements, Western blots and proteomics were used for the trypsin analysis. The cod larvae were reared under standard conditions at the Marine Research Institute, Stadur, Grindavík, Iceland. Larvae samples were collected daily during the first week post hatch (ph). Total protein extracts were prepared from pooled larvae samples. Trypsin activity was shown to be present at hatch followed by a decline with minimal activity observed at first feeding (day 3 ph). Western blot analysis of the early cod larvae strongly indicated the absence of trypsin at first feeding. Two dimensional electrophoresis (2DE) protein profiles of the cod larvae extracts were digitized and computer software was used to construct a composite reference gel. A mean of 422 protein spots (n = 4, SD = 6.21) with isolelectric points (pI) between 4 and 7 and molecular weights (MW) between 6 and 148 kDa were identified and their abundance monitored. All protein spots were recorded in terms of their pI, MW and abundance. 2DE gel analysis of isolated cod trypsin was performed and protein spots were excised from the gel and subjected to digestion followed by peptide separation by MALDI-TOF spectrometry. Peptide mass fingerprints (PMF) revealed two types of trypsins, cod trypsinogen I and trypsinogen X. Spots on 2DE gels of cod larvae matching the trypsin spots from isolated cod trypsins could not be identified as trypsins by PMF. Based on the data, we conclude that trypsins may be a critical factor for survival during the period when the cod larvae must initiate feeding or face starvation.