H (2)- and (13)C-breath tests are valuable non-invasive diagnostic tools for gastroenterological diseases. H (2)-breath tests are clinically established for the diagnosis of carbohydrate intolerance resulting from malabsorption (H (2)-breath tests with lactose, fructose, saccharose, sorbitol), of bacterial overgrowth (glucose H (2)-breath test) and for measurement of orcoceal transit time (lactulose H (2)-breath test). The (13)C-urea breath test is regarded as the "gold standard" procedure for the diagnosis of Helicobacter pylori infection. Moreover, (13)C-breath tests for measurement of gastric emptying can be considered as clinically established, meanwhile. (13)C-breath tests for the evaluation of pancreatic exocrine function or liver function can also be used clinically; however, they currently offer no substantial advantage over other diagnostic procedures. A major disadvantage of all breath tests is that they lack standardization although modifications of the test meal or solution, of the test performance and of the evaluation of data may markedly influence the results. Thus, this article presents the recommendations of the German Society of Neurogastroenterology and Motility and of the German Society of Digestive and Metabolic Diseases for clinically relevant H (2)- and (13)C-breath tests. Indications for the examinations, the procedures to be followed, the analysis of the obtained data and the conclusions to be drawn are delineated. The literature on which the recommendations are based is reviewed. However, personal experience of the authors is also taken into account since numerous questions regarding optimal test performance are not clarified by adequate studies.