A 14-week trial was conducted to investigate the effects of antinutritional factors (ANFs) commonly present in soybean ingredients, singly and in combination, on Atlantic salmon (Salmo salar L.) fed from start-feeding. The experimental diets consisted of a negative control fish meal diet (FM), and a positive control diet with 167 g kg À1 soybean meal inclusion (SBM) and four diets based on the FM diet supplemented with 2 g kg À1 soya-saponins (SAP), 1.5 g kg À1 isoflavones (IFL), 0.3 g kg À1 phytosterols (PHS) or a mixture of these (MIX). Fish fed the SAP diet showed significantly higher growth performance than those fed FM, while the IFL treatment significantly decreased growth performance of salmon fry. Fish fed the IFL diet had significantly lower maltase activity and higher trypsin activity in proximal intestine than fish fed the FM diet. Histological differences were observed in the liver of fish fed the IFL diet, characterized by reduced size of the hepatocytes. Fish fed the PHS and IFL diets showed the highest frequencies of skeletal deformities among the six treatments. In conclusion, the results indicate that purified isoflavones may negatively affect growth performance, intestinal function, liver metabolism and bone formation of salmon fry.