To investigate the cause of the changes in intestinal morphology and biliary bile status of rainbow trout Oncorhynchus mykiss fed defatted soybean meal (SBM)-based diets, casein-based semipurified diets supplemented with soya saponin, soya lectin, and cholyltaurine were fed to rainbow trout for 6 weeks. An unsupplemented control diet and a SBM-based diet were also tested as references. Poor development of microvilli and pinocytotic vacuoles, and accumulation of large vacuoles in the epithelial cells were observed in the distal intestine of fish fed diets containing saponin but not cholyltaurine. Hyperplastic connective tissue in the mucosal folds of the distal intestine was observed in fish fed a diet containing both saponin and lectin but not cholyltaurine. However, intestinal histological features in fish fed diet supplemented with cholyltaurine and lectin and/or saponin were similar to those in the control diet group. Liver morphology and biliary bile status were not affected by saponin and lectin. These results suggest that the abnormal features of the distal intestine of rainbow trout fed SBM-based diets are caused by the combination of soya saponin and soya lectin, and that supplemental cholyltaurine plays certain roles in normalizing the intestinal abnormalities caused by the saponin and lectin.