In the assessment of carbohydrate malabsorption, it is important to determine if a flat breath hydrogen test is a false negative result. Currently, the only reliable way to do this is with a lactulose test. We determined the reliability of assessing faecal hydrogen production as an indicator of an adequate in vivo hydrogen producing colonic bacterial flora. Unfortunately, the results clearly show that the incidence of falsely positive and negative faecal hydrogen production, when compared with in vivo lactulose testing, is so high that the simple faeces screening test is unsuitable for routine use. Until a simpler alternative is found, centres using the breath hydrogen test to determine carbohydrate malabsorption must continue to rely on lactulose breath testing when it is necessary to exclude potential false negative results.