Background: Limited data are available regarding the reproducibility of lactulose and fructose breath testing for clinical application in functional bowel disorders. Objectives: The purpose of this study was to investigate the reproducibility of lactulose and fructose breath hydrogen testing and assess symptom response to fructose testing. Methods: Results were analysed from 21 patients with functional bowel disorder with lactulose breath tests and 30 with fructose breath tests who completed another test >2 weeks later. Oro-caecal transit time, hydrogen responses, both qualitatively (positive/negative) and quantitatively (area under the curve (AUC) for hydrogen), were compared between tests. In another 36 patients, data scores for overall abdominal symptoms, abdominal pain, bloating, wind, nausea and fatigue were collected during the fructose test and compared to hydrogen responses. Results: No correlations were found for lactulose AUC (linear regression, p=0.58) or transit time (Spearman's p=0.54) between tests. A significant proportion (30%) lost the presence of fructose malabsorption (p0.05). Conclusions: Routine use of lactulose and fructose breath tests in functional bowel disorder patients is not supported due to its poor reproducibility and low predictive value for symptom responses.