Endogenous nitrogen and amino acid losses are associated with the digestion process. Different methods can be used to distinguish between gut endogenous and exogenous amino acid flows. These methods include feeding N‐free diets, the regression approach, the use of enzyme hydrolysed proteins coupled with ultrafiltra‐tion and the use of markers (e.g.,homoarginine, enzyme hydrolysed casein,15N‐labelled protein,15N‐leucine). All of the methods described have their limitations, but they have allowed major advances to be made in the measurement and understanding of endogenous amino acid secretion, reabsorption, flow and excretion.