Data are presented on scanning electron microscopy (SEM) on small intestinal biopsies of children with chronic diarrhea. In particular, there were 230 patients aged 3 months to 13 years with the following diagnoses: chronic nonspecific diarrhea, cow's milk protein intolerance, soy protein intolerance, giardiasis, cystic fibrosis, gluten-sensitive enteropathy, isolated lactase deficiency, isolated sucrase-isomaltase lactase deficiency, microvillus inclusion disease, rotavirus enteritis, protracted diarrhea of infancy, chylomicron retention disease, visceral myopathy and villous asthenia. Examination of biopsied intestinal mucosa by SEM has yielded important new information and insights on structural pathology and ultrastructural topography. Many of the observed changes helped to better understand the pathophysiology of some of the diarrheal disorders. SEM was also able to detect new features such as mycoplasma-like microorganisms and the absence of the glycocalyx. To adequately assess small bowel mucosal pathology at the ultrastructural level, scanning electron microscopy is an indispensable tool.