Two experiments were conducted to determine apparent ileal digestibility of amino acids (AIDAA) and nitrogen (AIDN) in cottonseed meal (CSM) and soyabean meal (SBM) fed to growing pigs. In the first experiment, twenty-four male pigs (37.3 (SE 2.7) kg) were individually penned and randomized to either CSM or SBM diets. The diets contained 40% of the protein meal (either CSM or SBM) in a wheat starch-sucrose (1:1, w/w) base containing vitamins and minerals, and Cr2O3 as an indigestible marker. Pigs were acclimated to the experimental diets over a 3 d period and on day 4 through to day 14 were offered 1800 g/d of the diet. Diets were offered in three meals/d from day 4 to day 11 and in eight meals/d from day 12 to day 13. After the eighth hourly-meal on day 14, twelve pigs were anaesthetized with halothane while the remaining twelve pigs were CO2-stunned and processed using commercial slaughter procedures. Ileal digesta were collected from a 1500 mm portion of the terminal ileum of each pig and subsequently analysed for amino acids, N, organic matter and Cr. Results indicated that AIDAA of CSM and SBM were lower when digesta were collected following CO2-stunning than when digesta were obtained under halothane anaesthesia. Consistently, AIDN in CSM (0.51 v. 0.56) and SBM (0.55 v. 0.71) were lower (P < 0.05) in CO2-stunned pigs than in halothane-anaesthetized pigs. Furthermore, when digesta collection was conducted under halothane anaesthesia, AIDN of CSM was lower (P < 0.001) than that of SBM. In the second experiment, six male pigs (45 (SE 2.6) kg) were fitted with T-piece cannulas implanted in the terminal ileum, housed individually in metabolism cages, and randomly allocated to either CSM or SBM diets in a single reversal arrangement. Ileal digesta were collected for AIDAA and AIDN determination. Although statistical comparisons could not be made between the two experiments, the AIDAA and AIDN data obtained via cannulated pigs were similar to those values obtained using the halothane-anaesthesia method. Overall, the CO2-stunning method is not recommended for studies of amino acid or nitrogen ileal digestibilities, but may be useful for the study of other dietary constituents.