The present study was designed to evaluate if genetically modified (GM) maize (Bt maize, event MON810) compared with the near-isogenic non-modified (nGM) maize variety, added as a starch source at low or high inclusions, affected fish health of post-smolt Atlantic salmon, Salmo salar L. To evaluate the health impact, selected stress- and immune-response biomarkers were quantified at the gene transcript (mRNA) level, and some also at the protein level. The diets with low or high inclusions of GM maize, and its near-isogenic nGM parental line, were compared to a control diet containing GM-free suprex maize (reference diet) as the only starch source. Total superoxide dismutase (SOD) activity in liver and distal intestine was significantly higher in fish fed GM maize compared with fish fed nGM maize and with the reference diet group. Fish fed GM maize showed significantly lower catalase (CAT) activity in liver compared with fish fed nGM maize and to the reference diet group. In contrast, CAT activity in distal intestine was significantly higher for fish fed GM maize compared with fish fed reference diet. Protein level of heat shock protein 70 (HSP70) in liver was significantly higher in fish fed GM maize compared with fish fed the reference diet. No diet-related differences were found in normalized gene expression of SOD, CAT or HSP70 in liver or distal intestine. Normalized gene expression of interleukin-1 beta in spleen and head-kidney did not vary significantly between diet groups. Interestingly, fish fed high GM maize showed a significantly larger proportion of plasma granulocytes, a significantly larger sum of plasma granulocyte and monocyte proportions, but a significantly smaller proportion of plasma lymphocytes, compared with fish fed high nGM maize. In conclusion, Atlantic salmon fed GM maize showed some small changes in stress protein levels and activities, but none of these changes were comparable to the normalized gene expression levels analysed for these stress proteins. GM maize seemed to induce significant changes in white blood cell populations which are associated with an immune response.