Atlantic salmon develop subacute enteritis in the distal intestine (DI) when fed diets containing soybean meal (SBM) at high levels, a condition accompanied by increased trypsin activity in the DI intestinal content compared to fish fed conventional fishmeal (FM) based diets. To further investigate the responses of Atlantic salmon to dietary SBM, we measured trypsin activity in intestinal contents, quantified pancreatic trypsin mRNA expression, surveyed trypsin mRNA expression in selected tissues and characterized active forms of trypsin in the intestinal wall and brain. Enzyme measurements showed that trypsin activity in the intestinal content of SBM fed fish was lower in the proximal segments of the intestine, but higher in the DI compared to FM fed fish. The difference in enzyme activity was not reflected in a differential expression of pancreatic trypsin mRNA between fish fed the different diets (FM or SBM). Trypsin mRNA was expressed in 18 different tissues (esophagus, stomach, pancreas, pyloric tissue, midintestine, distal intestine, liver, head kidney, kidney, heart, spleen, thymus, brain, eye, gills, gonads, muscle and skin) but was most prominently expressed in tissues of the gastrointestinal (GI) tract and brain. We report for the first time an upregulation of trypsin-like activity in the DI wall using an in-gel trypsin activity assay, as well as modulated activity in the brain of fish fed SBM. The increased activity in the DI wall may contribute to disease severity and higher trypsin activity in the intestinal content.