The effect of extrusion of soyabean seeds and sulphur amino acid (AA) supplementation on trypsin inhibitor (TI) and lectin activity, and on the histology and microbiology of the jejunum were studied. Wistar rats were fed semi-purified diets containing 10% of soyabean seeds: raw (R) or extruded at 160°C (E) and unsupplemented or supplemented with 0.3% (AA) (met+cys, 1:1). Extrusion reduced TI activity in seeds from 25.0 to 11.8 TUI/mg. Extrusion of soyabean seeds also reduced agglutination activity against human red blood cells from 1:1600 to 1:100 (group AB), from 1:800 to 1:100 (group 0), from 1:800 to 1:50 (group A), and from 1:400 to 1:50 (group B). Extrusion of soyabean seeds improved (P < 0.05) performance and decreased pancreas weight (0.40 vs 0.50% BW). Extrusion increased (P < 0.05) pancreatic trypsin activity (3495 vs 5901 U/100 g protein), improved the morphology of the jejunum, and reduced the E. coli count. The influence of AA in the group fed raw seeds on performance and morphological gut parameters was even better than the effect of extrusion.