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In the current experiment, RNA was isolated from the distal intestine (DI) of Atlantic salmon-fed fishmeal-based diets containing either genetically modified (GM) maize (Bt maize, Mon810 Ò , Monsanto Company, St. Louis, Missouri, USA) or its conventional near-isogenic parental line (non-GM) for 82 days, both at 300 g kg )1 inclusion. From a suppression subtractive hybridization (SSH) cDNA library, 192 clones with similarity to both known and novel Atlantic salmon sequences were identified. Real-time PCR was used to study the differential expression of 10 clones between the dietary groups. Expression of a clone showing high protein similarity to proton-dependent high-affinity oligopeptide transporter was significantly upregulated in fish-fed GM maize compared with fish-fed non-GM maize. No significant differences in expression were observed for the nine other clones showing similarity to the following proteins: heat shock protein 90B, procathepsin B, interferon gamma-inducible protein 30, ferritin heavy subunit, serum lectin isoform/C-type mannosebinding lectin, fatty acid-binding protein/gastrotropin, ATP synthase [H+ transporting, mitochondrial F0 complex, subunit c (ATPSYNT)], sonic hedgehog and translationally controlled tumour protein. In conclusion, only minor differences in DI transcriptional gene expression was observed between fish fed the GM and non-GM maize diets. KEY WORDS