Despite extensive use in clinical practice, difficulties regarding interpretation of hydrogen breath test are still very frequent, even on research grounds. After the administration of a non-absorbable sugar, such as lactulose, an increase of breath hydrogen and methane is evident; this phenomenon is considered an index of colonic fermentation. It is not clear, however, if the levels of these compounds correlate with the presence and severity of functional symptoms, nor if they accurately reflect gas production at colonic level. So far, apart from flatulence, we have no indications regarding the ability of hydrogen or methane to act as biomarkers of intraluminal events. On the other hand, it has been shown that in functional bowel disease a colonic dysbiosis exists, and that the modification of bacterial flora might result in a reduction of symptom severity. Consequently, it is not clear if hydrogen and methane colonic production could have a role in the pathophysiology of functional complaints, but it is possible that other fermentation products should be taken into consideration, such as acetate, propionate, and alcohol.