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Bacterial enzymes are responsible for degradation of beta-aspartyl peptides in the intestinal tract. These peptides, especially the dipeptide beta-aspartylglycine, are useful as indicators of an impaired anaerobic intestinal microflora of antibiotic-treated patients. A method to separate the dipeptides beta-aspartylalanine, beta-aspartylglutamine, beta-aspartylglycine and beta-aspartylserine, using reversed-phase high-performance liquid chromatography and precolumn derivatization with phenyl isothiocyanate, was developed. This method was used to determine beta-aspartylpeptidase activity in faecal supernatants of healthy human volunteers and antibiotic-treated patients with beta-aspartylglycine as substrate. This activity was absent in the antibiotic-treated group, while in individuals with an intact intestinal flora it ranged from 16 to 100% degradation per 18 h. In addition, it was found that faecal enzyme preparations cleaved beta-aspartylglycine at a much lower rate than the other beta-aspartyl peptides.