Analysis of breath specimens for volatile metabolites of orally administered substrates offers a simplified detection method for the presence of an abnormal small-intestinal flora. This technique is not only simpler and more acceptable to patients than jejunal aspiration, but also gives quicker information to the clinician than microbiologic culture of the jejunal aspirate. Experience with a probe which is usually completely absorbed before the colon is reached (1 g 14C-xylose) has demonstrated better test sensitivity (separating normal from abnormal) and test specificity (separating bacterial overgrowth from small-bowel malabsorption) than that seen with a probe which normally has substantial passage of substrate to the colonic bacteria (as seen with the 14C-bile acid breath test). Ongoing evaluation of nonradioactive probes (H2 generation from fermentable carbohydrate, 13CO2 generation from 13C-labeled substrate similar to the principle of the 14C-xylose breath test) offers promise for use of bacterial overgrowth breath tests in children and reproductive-age females.