Breath tests are a simple and safe alternative to more invasive investigation strategies for many gastroenterological conditions. Both the hydrogen breath tests and the new 13C stable radioisotope breath tests are nonradioactive and safe in children and pregnancy. The range of diseases that can be identified include Helicobacter pylori infection, lactose and fructose intolerance, bacterial overgrowth, bile salt wastage, pancreatic insufficiency, liver dysfunction, and abnormal small bowel transit. In this review, the physiology supporting these tests and the principles of normal gas dynamics in the gut are briefly reviewed and then related to the test preparation and interpretation in two parts: 1) detection of H. pylori and 2) small bowel, pancreatic, and hepatobiliary disorders. A MEDLINE search reviewing all English language abstracts from 1966 to March, 2001 was performed, with an additional review of abstracts from major national meetings from 1997 to 2001. Using the information from this review, the performance characteristics of the various tests were detailed, and an attempt is made to provide some literature-based guidance regarding their indications and limitations. The interpretation of “flat” breath tests and the selective use of methane collection and colonic alkalinization are discussed. Breath tests are valuable tools that are, in general, underutilized in evaluating dyspepsia and functional bloating and diarrhea, as well as suspected malabsorption, including lactose intolerance.