To investigate the cause of morphological changes occurring in the liver and intestine of rainbow trout Oncorhynchus mykiss fed defatted soybean meal (SBM)-based non-fish meal diets, morphological observations were conducted on fish fed casein-based semipurified diets supplemented with soybean antinutritional factors (soya saponin, soya isoflavone, soya lectin, oligosaccharide, Ca-phytate and their mixture). Hepatocytes and the epithelial cells in the hepatic ducts were not atrophied in any of the treatments. Lack of microvilli and pinocytotic vacuoles, and fatty degeneration of the epithelial cells were observed in the distal intestine of fish fed diets containing soya saponin. The proliferation of connective tissue in the mucosal folds and submucosa was shown in the distal intestine of fish fed the diet containing all substances including lectin. These results suggest that both saponin and lectin are the responsible factors in SBM for the occurrence of morphological changes of the distal intestine in rainbow trout fed SBM-based diets.