The effect of extrusion of faba bean seeds and supplementation of sulphur amino acids (AA) on trypsin inhibitor (TI) and lectin activity, and the histology and microbiology of the jejunum were studied. Male Wistar rats were fed semi-purified diets containing 10% faba bean seeds, either raw (R) or extruded at 160°C (E); the diets were either unsupplemented or supplemented with 0.3% sulphur AA (met + cys, 1:1). Extrusion reduced TI activity of seeds from 1.8 (FR) to 0.5 with TlU/mg (FE) and completely eliminated agglutination activity against human red blood cells (RBC). Extrusion of faba bean seeds did not affect rat performance or pancreatic trypsin activity (5255 vs 4065 U/ 100 g protein), and decreased (P < 0.05) dry matter digestibility (89.7 vs 92.9%). Supplementing sulphur amino acids improved performance of rats fed both raw and extruded seeds. Extrusion of faba bean and supplementing sulphur amino acids significantly improved intestinal crypt depth, villi length and width