Protracted diarrhea is a clinical entity characterized by diarrhea lasting greater than 2 weeks, starting before 3 months of age, with severe nutritional aggravation and negative stool culture for enteropathogens. This report deals with the ultrastructural abnormalities found in the intestinal mucosa of children with protracted diarrhea. Forty children (mean age 5.1 months) were studied. They were submitted to the following tests of intestinal function: D-xylose, triglyceride tolerance, small bowel biopsy (light and electron microscope), sigmoidoscopy, and sweat test. D-Xylose absorption and triglyceride tolerance test in these patients were both significantly lower than controls. Ultrastructural analysis of the small bowel of 12 patients showed various degrees of alterations, mainly shortening of the microvilli, increased number of multivesicular bodies, and vacuolation of mitochondria and endoplasmic reticulum. These lesions were totally reversible after clinical and nutritional recovery as could be proven in two children. The most common cause of protracted diarrhea in these patients was secondary carbohydrate intolerance and dietary protein cow's milk and soy bean intolerance, which resulted in colitis or malabsorption as a consequence of intestinal mucosa injury due to acute gastroenteritis.