AbstractStandard soybean meal, heat treated to differing degrees and containing varying levels of soybean lectin and trypsin inhibitor, was used to study the effect of soybean‐containing diets on the morphology of the distal intestine in Atlantic salmon,Salmo salarL. A reference diet based on fish meal and a fish meal diet mixed with an alcohol extract of soybean meal were used. The fish (145 g) were kept in 27 m3net pens (200 fish per pen) in sea water with an average temperature of 11 °C for 12 weeks. Whereas a normal morphology of the distal intestine was seen in the fish fed the reference diet, all soybean diets caused alterations in the distal intestine irrespective of heat treatment. Similar changes were observed with the diet which had added alcohol solubles. It is concluded that alcohol‐soluble components in the soybeans are responsible for the observed changes. It cannot be determined which of the soybean antinutrients is causing the alterations from the present study. Oligosaccharides and saponines are possible candidates. However, the possibility that unknown antinutrients are affecting the salmon intestine should not be overlo