Breath tests (BT) represent a valid and non-invasive diagnostic tool in many gastroenterological disorders. Their wide diffusion is due to the low cost, simplicity and reproducibility and their common indications include diagnosis of carbohydrate malabsorption, Helicobacter pylori infection, small bowel bacterial overgrowth, gastric emptying time and orocaecal transit time. The review deals with key points on methodology, which would influence the correct interpretation of the test and on a correct report. While a clear guideline is available for lactose and glucose breath tests, no gold standard is available for Sorbitol, Fructose or other H2 BTs. Orocaecal transit time (OCTT) defined as time between assumption of 10 g lactulose and a peak > 10 ppm over the baseline value, is a well-defined breath test. The possible value of lactulose as a diagnostic test for the diagnosis of small bowel bacterial overgrowth is still under debate. Among (13)C breath test, the best and well characterized is represented by the urea breath test. Well-defined protocols are available also for other (13)C tests, although a reimbursement for these tests is still not available. Critical points in breath testing include the patient preparation for test, type of substrate utilized, reading machines, time between when the test is performed and when the test is processed. Another crucial point involves clinical conclusions coming from each test. For example, even if lactulose could be utilized for diagnosing small bowel bacterial overgrowth, this indication should be only secondary to orocaecal transit time, and added into notes, as clinical guidelines are still uncertain.