Elevated antibody levels against the yeast Saccharomyces cerevisiae have been reported in sera from patients with Crohn's disease and not with ulcerative colitis. The aim of the study was to identify the nature of the epitopes supporting this antibody response. Whole cells from different S. cerevisiae strains were selected in immunofluorescence assay for their ability to differentiate the antibody responses of patients with Crohn's disease and ulcerative colitis. Their cell wall phosphopeptidomannans were then tested as antigen in enzyme-linked immunosorbent assay (ELISA) against sera from 42 patients with Crohn's disease, 20 patients with ulcerative colitis, and 34 healthy controls. Graded chemical degradations were performed on the most reactive strain phosphopeptidomannan. The discriminating epitope was determined through gas-liquid chromatography-mass spectrometry. The greatest discrimination among patients with Crohn's disease, ulcerative colitis, and controls was obtained with Su1, a S. cerevisiae strain used in brewing of beer. ELISA directed against phosphopeptidomannan of this strain was 64% sensitive and 77% specific for discriminating Crohn's disease versus ulcerative colitis and 71% sensitive and 89% specific for Crohn's disease versus controls. Periodate oxidation and selective degradation demonstrated that the most important polysaccharide epitope was shared by both the acid-stable and the alkali-labile domains of the phosphopeptidomannan. The determination of oligomannose sequences of S. cerevisiae Su1 phosphopeptidomannans suggested that a mannotetraose, Man (1 --> 3)Man(1 --> 2)Man(1 --> 2)Man, supported the serological response seen in Crohn's disease. Further identification of the immunogen eliciting this antibody response as a marker of the disease may help to understand its etiology.