The effects of extruding soya bean, faba bean and pea seeds on trypsin inhibitor (TI) and lectin activities, dry matter and protein digestibilities, pancreatic trypsin activity, relative weight of rat internal organs, and microbiology and histology of the jejunum were studied. Wistar rats were fed semipurified diets containing 10% of legume seeds: raw (R) or extruded at 150°C (E). Extrusion reduced TI activity of soya bean seeds from 31.3 to 23.0, faba bean from 2.1 to 0.7, and pea from 2.3 to 0.3 TlU/mg. Extrusion of soya bean seeds also reduced agglutination activity against guinea pig erythrocytes. Extrusion of soya bean, but not of pea and faba bean, improved apparent digestibility of dry matter and protein (P≤0.01). Pancreas weight (0.392% BW) and trypsin activity (0.424 U/total pancreas) were the highest in rats fed the diet with raw soya bean. Extrusion increased (P≤0.05) trypsin activity in the pancreas of rats fed on all seeds (mean value 2777 vs 3212 U/100 g protein) and decreased (P≤0.05) total protein content (mean 13.0 vs 10.6 mg/pancreas) as well as the relative weight of the pancreas. Significant differences were found between the relative weights of several organs in rats fed on pea, faba bean or soya bean diets. Extrusion of faba bean reduced the E. coli count in the small intestine and tended to decrease damage to intestinal villi.