The aim of the study was to determine whether the specificity of the [14C]d-xylose breath test could be improved, by excluding false-positive tests due to premature colonic metabolism of the [14C]d-xylose caused by rapid colonic transit. Forty-seven patients with suspected small bowel bacterial overgrowth were investigated by (1) aspiration and culture of duodenal fluid and (2) a [14C]d-xylose breath test. Those with either a positive duodenal culture or breath test had a repeat [14C]d-xylose breath test given with one of three transit markers (barium, Gastrografin or 99mTc-labeled tin colloid) to determine if the site of metabolism was in the small bowel or colon. Fourteen patients had positive duodenal cultures, four of whom had a negative [14C]d-xylose breath test, 15 patients had a positive [14C]d-xylose breath test, three of which were due to colonic metabolism of the xylose. Where transit markers were used, 14C was detectable in the breath and serum before barium had entered the small bowel, thus the barium did not comigrate with the xylose. Gastrografin accelerated small bowel transit, leading to malabsorption of the xylose in the small intestine and subsequent colonic metabolism of the xylose. 99mTc-labeled tin colloid had no obvious disadvantages and appeared to be the marker of choice. The use of a transit marker increased the specificity of the [14C]d-xylose breath test from 85% to 94%. The specificity of the [14C]d-xylose breath test for the detection of small bowel bacterial overgrowth is improved to greater than 90% by the use of an appropriate transit marker.