Four German Friesian cows, fitted with cannulas in the rumen, duodenum and ileum, were fed on diets containing similar amounts of rumen-degradable organic matter and crude protein, and soyabean meal or fish meal as the major protein source. The disappearance of organic matter, nitrogen and amino acids (AA) from the stomachs and from the small and large intestines was determined. Digestibilities of organic matter, nitrogen and AA in the stomachs were similar for both diets. A trend was observed for greater disappearance of these components from the small intestine of cows fed the fish meal diet. The comparison of the AA composition of duodenal digesta with that of the diets indicated that ruminal fermentation altered the AA profile of fish meal less than that of soyabean meal. Disappearance of individual AA from the small intestine differed within and between diets. Preferential disappearance of essential AA from the small intestine compared with non-essential AA was observed. We conclude that the protein value of feedstuffs in terms of absorbed AA should be evaluated separately for feedstuff and individual AA.