BACKGROUND: Perinuclear antineutrophil cytoplasmic autoantibodies (pANCA) are a well recognised marker for ulcerative colitis. Antibodies to oligomannosidic epitopes of the yeast Saccharomyces cerevisiae (ASCA) are a new marker associated with Crohn’s disease. AIMS: To assess the value of detecting pANCA and/or ASCA for the diagnosis of ulcerative colitis and Crohn’s disease. METHODS: Serum samples were obtained from 100 patients with Crohn’s disease, 101 patients with ulcerative colitis, 27 patients with other miscellaneous diarrhoeal illnesses, and 163 healthy controls. Determination of pANCA and ASCA was performed using the standardised indirect immunofluorescence technique and an ELISA, respectively. RESULTS: The combination of a positive pANCA test and a negative ASCA test yielded a sensitivity, specificity, and positive predictive value of 57%, 97%, and 92.5% respectively for ulcerative colitis. The combination of a positive ASCA test and a negative pANCA test yielded a sensitivity, specificity, and positive predictive value of 49%, 97%, and 96% respectively for Crohn’s disease. Among patients with miscellaneous non-inflammatory bowel disorders, three were ASCA positive and two were pANCA positive. One control was ASCA positive. The presence of ASCA in patients with Crohn’s disease was associated with small bowel involvement. CONCLUSION: ASCA and pANCA are strongly associated with Crohn’s disease and ulcerative colitis, respectively. Combination of both tests could help the diagnosis of inflammatory bowel disease.