Unsuspected bacterial contamination of the small intestine was indicated by breath hydrogen testing in nine patients aged 2 to 34 months during physical examinations for chronic diarrhea and abdominal pain. Elevated bacterial counts of questionable significance were found in duodenal aspirates before and after antibiotic treatment. There was no evidence of bile salt deconjugation or structural changes in the small intestine by light or electron microscopy. This may indicate that the site of colonization is distal to the biopsy site. Breath testing indicated lactose malabsorption in all patients, and four of five patients tested also malabsorbed sucrose. Duodenal disaccharidase levels in all patients were within the normal ranges, but in eight patients the lactase-sucrase ratio was greatly elevated (0.80 +/- 0.36; normal less than 0.45). Dietary restriction alone did not cause complete cessation of symptoms, whereas all patients responded dramatically to oral antibiotic therapy. When patients were well, the lactase-sucrase ratio had returned to normal in those tested, and all nine had normal lactose and lactulose breath hydrogen tests. Unsuspected bacterial contamination of the small intestine, which is easily detected using the breath hydrogen test, may be more commonly associated with chronic diarrhea in children than has been previously realized. In such cases, therapy should be directed at removing the contamination.