Breath hydrogen testing for assessing the presence of carbohydrate malabsorption is frequently applied to refine dietary restrictions on a low fermentable carbohydrate (FODMAP) diet. Its application has also been extended for the detection of small intestinal bacterial overgrowth. Recently, several caveats of its methodology and interpretation have emerged. A review of the evidence surrounding its application in the management of patients with a functional bowel disorder was performed. Studies were examined to assess limitations of testing methodology, interpretation of results, reproducibility, and how this relates to clinical symptoms. A wide heterogeneity in testing parameters, definition of positive/negative response, and the use of clinically irrelevant doses of test carbohydrate were common methodological limitations. These factors can subsequently impact the sensitivity, specificity, and false positive or negative detection rates. Evidence is also increasing on the poor intra-individual reproducibility in breath responses with repeated testing for fructose and lactulose. On the basis of these limitations, it is not surprising that the diagnosis of small intestinal bacterial overgrowth based on a lactulose breath test yields a wide prevalence rate and is unreliable. Finally, symptom induction during a breath test has been found to correlate poorly with the presence of carbohydrate malabsorption. The evidence suggests that breath hydrogen tests have limited clinical value in guiding clinical decision for the patient with a functional bowel disorder.