Aquaculture is promising in increasing the amount of fresh Atlantic cod available all year around. The aim of this study was to investigate the effects of pre-rigour filleting on fillet quality of wild and farmed cod. Pre-rigour filleting resulted in significantly less fillet gaping than in fillets produced post rigour. The pre-rigour fillets were, however, 12–13% shorter post rigour. In spite of the significantly lower water content of the muscle 6 days post mortem, a significantly higher liquid loss was seen in the pre-rigour group. Differences in gaping score and muscle pH were dependent on whether the fish were wild or fed. Fillet gaping increased with storage time and was particularly pronounced for well-fed cod. Fed cod had a significantly higher hydroxyproline (Hyp) content and significantly lower amount of glycosaminoglycans (GAGs) than wild cod. The ratio between GAGs and Hyp was thus significantly lower in fed cod. A connection between connective tissue components and fillet gaping may exist. However, further investigations are required.