Impaired growth, immunity, and intestinal barrier in mammals, poultry, and carp have been attributed to the mycotoxin deoxynivalenol (DON). The increased use of plant ingredients in aquaculture feed implies a risk for contamination with mycotoxins. The effects of dietary DON were explored in 12-month-old Atlantic salmon (Salmo salar) (start weight of 58 g) that were offered a standard feed with non-detectable levels of mycotoxins (control group) or 5.5 mg DON/kg feed (DON group). Each group comprised two tanks with 25 fish per tank. Five fish from each tank were sampled eight weeks after the start of the feeding trial, when mean weights for the control and DON groups were 123.2 g and 80.2 g, respectively. The relative expression of markers for three tight junction proteins (claudin 25b, occludin, and tricellulin) were lower, whereas the relative expression of a marker for proliferating cell nuclear antigen was higher in both the mid-intestine and the distal intestine in fish fed DON compared with fish from the control group. The relative expression of markers for two suppressors of cytokine signaling (SOCS1 and SOCS2) were higher in the distal intestine in fish fed DON. There was no indication of inflammation attributed to the feed in any intestinal segments. Our findings suggest that dietary DON impaired the intestinal integrity, while an inflammatory response appeared to be mitigated by suppressors of cytokine signaling. A dysfunctional intestinal barrier may have contributed to the impaired production performance observed in the DON group.