Typically, in vitro methods used for estimating the amount of ileal digestible AA do not exhaustively digest samples, and arbitrary methods for separating digestible from indigestible protein are used. This may lead to over- or underestimation of digestibility coefficients. A method that exhaustively digests proteins using pepsin and pancreatin was developed, and the first objective of this research was to confirm that exhaustive digestion was indeed appropriate and to determine the fractionation method for separating digestible from indigestible proteins. For this, three homoarginine-labeled animal proteins were prepared. Samples were subsequently digested in vivo and in vitro to determine which fraction should be considered indigestible, and in vitro followed by in vivo to determine whether the extent of digestion in vivo was improved by predigestion. In vivo, soluble but unabsorbed peptides were smaller than 1 kDa, suggesting that the size of soluble peptides is not what prevents their absorption. Thus, all in vitro-soluble proteins should be considered digestible. In vitro, 88 +/- 3% of the soluble peptides were smaller than 1 kDa, with the remainder between 1 and 5 kDa, suggesting that in vitro digestion is less complete. Predigested samples were digested in vivo to the same size distribution as the nonpredigested samples. The second objective was to test whether in vitro digestibility assays based on these principles equaled in vivo digestibility. For this, digestibility data for 25 animal proteins were compared. Results showed a lack of correlation between lysine digestibility coefficients; however, across samples, the extent of digestion did not differ for lysine (P = 0.71), threonine (P = 0.26), methionine (P = 0.18), or valine (P = 0.66), whereas in vitro digestibility coefficients were lower for (the less water-soluble) histidine (P = 0.05), isoleucine (P < 0.01), leucine (P < 0.01), and phenylalanine (P = 0.05). In conclusion, in vitro digestibility assays should exhaustively digest proteins to mimic in vivo digestibility. All in vitro-soluble peptides could be considered digestible, because in vivo, no large soluble peptides were observed whose size prevented them from being absorbed. However, an in vitro assay based on these principles lacked precision for highly water-soluble AA, and underestimated digestibility for other AA. Better solubilization of the digesta and more replicates may improve the in vitro assay further.