The study determines the prevalence and clinical significance of small intestinal bacterial overgrowth (SIBO) in coeliac disease and investigates the relationship between fasting breath hydrogen (FBH2), SIBO and small intestinal transit in coeliac patients. The glucose hydrogen breath test was used to screen for SIBO and positive results were confirmed by quantitative small intestinal aspirate culture. Two out of 25 untreated patients and one out of 30 patients on a gluten-free diet had SIBO. Bacterial overgrowth was not associated with any apparent clinical sequelae, and antibiotic therapy was not necessary. Coeliac patients with severe histological enteropathy had higher FBH2 levels (17.0 ppm) than coeliac patients with near normal histology, normal individuals, or disease controls (7.2, 9.7 and 8.2 ppm, P = 0.002, 0.01 and 0.003, respectively). Small intestinal bacterial overgrowth did not account for this increase in FBH2 levels, as significant differences remained when coeliac patients with SIBO were excluded from the analysis. There was no correlation between FBH2 and mouth-to-caecum transit time (lactulose hydrogen breath test). These findings show that SIBO and abnormal small intestinal motility do not explain the elevation of FBH2 in coeliac disease. Breath hydrogen concentrations correlated most closely with the severity of histological enteropathy and the presence of symptomatic diarrhoea.