Atlantic salmon Salmo salar were fed fish feeds based on 100% replacement of fish oil (FO) with plant oil (PO) as compared to a 100% FO‐based diet. The transcript levels of eight genes’ encoding proteins involved in the cellular response to stressors [metallothionein‐A isoform (MT‐A), cytochrome P450 1A (CYP1A), heat‐shock protein 70 (HSP70), catalase (CAT), glutathione S‐transferase (GST), glutathione reductase (GR), proliferating cell nuclear antigen (PCNA) and caspase 6A] were quantified and compared to cell division (% PCNA‐positive cells) and apoptosis [% terminal transferase mediated dUTP nick end labelling technique (TUNEL)‐positive cells] in the mid intestinal (MI) section of the gastrointestinal tract. Five of these genes were also quantified in the pylorus caeca region (PR). Fish fed 100% PO‐based diets had significantly lower density of both PCNA and TUNEL‐positive cells in the MI section compared to fish fed a 100% FO‐based diet. The transcription levels of GST and caspase 6A were found to be significantly lower in the MI section of individuals fed a PO‐based diet compared to a FO‐based diet, analysed by a t‐test. In the PR, GR expression was significantly lower in the PO group compared to the FO group. The apoptosis markers PCNA and TUNEL were lower in the group fed a PO‐based diet. The results suggest that the transcription levels of three of the studied genes, GST, caspase 6A and GR, can be used as indicators of the MI response to feeding S. salar a PO‐based diet.