N-epsilon-(gamma-glutamyl)-lysine is a crosslinking amino acid formed in food mainly during treatment with microbial transglutaminase (mTG). The purpose of this study was to investigate to which amount isopeptides are detectable in a low-molecular weight peptide fraction after simulated gastrointestinal digestion. Casein, which had been enriched with N-epsilon-(gamma-glutamyl)-lysine by mTG to different extents, was subjected to simulated gastrointestinal digestion and the resulting peptide mixture fractionated into a low- and a high molecular weight fraction (below or above 200-500 Da, respectively) using semipreparative gel permeation chromatography. N-epsilon-(gamma-glutamyl)-lysine was analysed in these fractions by RP-HPLC after enzymatic hydrolysis and derivatisation with phenyl isothiocyanate. N-epsilon-(gamma-glutamyl)-lysine was found nearly exclusively in the high-molecular weight fraction, indicating that dietary N-epsilon-(gamma-glutamyl)-lysine present in mTG-modified food proteins is not available for absorption in the intestine.