Comparisons were recently made between the discovery of H. pylori as a cause of peptic ulcer disease and bacterial overgrowth in IBS. This perception is based on the dramatic shift in thinking accompanying the concept that some cases of IBS may be bacterial in origin. However, the case for bacterial overgrowth in IBS may not altogether contradict the convention or negate the accumulated discoveries in IBS as a first glance may suggest. For example, it is well known that bacterial endotoxin results in rectal hyperalgesia similar to IBS (Am J Physiol 2000;279:G781–G790). The long reported psychological attributes of IBS could also have a connection to intestinal colonization because data suggest that increases in CRF, a byproduct of stress, result in a reduction of intestinal migrating motor complexes (Peptides 1986;7:73–77). A reduction in these complexes is known to result in bacterial overgrowth (J Clin Invest 1977;59:1159–1166, Ann Surg 1998;228:188–193, Dig Dis Sci 2002;47:2639–2643). Therefore, the concept of bacterial overgrowth in IBS may simply be another piece of the IBS puzzle. To address more specific concerns, there is much discussion over the efficacy of lactulose breath testing in diagnosing bacterial overgrowth. Although culture is the gold standard for most bacterial processes, given the length of the small bowel, sampling a single area is likely to underestimate the presence of bacterial overgrowth. In fact, there are tremendous limitations to small intestinal cultures, which include: (1) the lack of appropriate instruments to acquire culture specimens; (2) the low quantity of usually aspirated fluid; (3) the requirement for special techniques to preserve anaerobes; and (4) only 20% of the gut flora are even culturable (Hart AL, Stagg AJ, Graffner H, Glise H, Falk P, KammGut MA. Ecology. London: Martin Dunitz Ltd, 2002). With these limitations, indirect techniques cannot be validated against this less than perfect “gold” standard. Another concern is how bacterial overgrowth or abnormal breath testing can explain both diarrhea and constipation in IBS. Two studies now suggest an association between methane on breath test and constipation (Dig Dis Sci 2003;48:89–92, Am J Gastroenterol 2003;98:412–419). Although one possibility may be that constipation favors intestinal methanogenic proliferation, we have published data to suggest that methane gas itself may contribute. When canine small intestine is perfused with methane, a 75% reduction in transit is observed compared with transit during the perfusion with room air (Neurogastroenterol Motil 2002;4:437). Although these data are preliminary, they are very intriguing and warrant further investigation. Much of the current sentiment on this new concept in IBS has become a debate of terminology. What does an abnormal breath test mean? Is it small intestinal bacterial overgrowth? Is it colonic fermentation? More work is needed to answer these questions. However, this debate should not detract the clinical message: (1) there is a higher prevalence of abnormal breath test in IBS patients compared with controls; and (2) antibiotic treatment of IBS improves symptoms in a fashion that is highly dependent on the normalization of the lactulose breath test abnormalities (Am J Gastroenterol 2003;98:412–419).