Breath hydrogen (H2) measurements are applied in clinical medicine for the detection of carbohydrate malabsorption. H2 in expired air results when dietary sugars escape absorption in the small intestine, thereby becoming available for bacterial fermentation. H2 produced by bacterial metabolism of the carbohydrate is absorbed into the portal circulation and excreted in breath. Relatively simple collection, storage, and analysis methodologies have been developed in recent years. They permit convenient and noninvasive testing of patients in most age groups for common clinical disorders of digestion and absorption, including lactase deficiency and other disorders of di- and mono-saccharide malabsorption, starch malabsorption, and small bowel bacterial overgrowth. Limitations of breath hydrogen testing are few. Developmental considerations constrain the ease of interpretation of breath H2 measurements in early infancy, and factors affecting intraluminal H2 production by the intestinal flora may occasionally affect the H2 signal. Despite these factors, breath H2 testing has repeatedly been demonstrated to be the most accurate indirect indicator of lactase deficiency, and breath H2 measurements have been widely applied in studying digestion of the entire spectrum of dietary carbohydrates.