SummaryThe pathophysiology of diarrhea, especially in the otherwise healthy child, is still poorly understood. The aim of this study was to use the scanning electron microscope (SEM) to examine the surface of the jejunal mucosa of children with chronic nonspecific diarrhea (CNSD) (n = 9) and to compare the findings with specimens obtained from children with (n = 21) and without (n = 11) other gastrointestinal diseases. Light microscopy of the specimens from children with CNSD was normal. However, SEM showed the presence of bacterial colonization with predominantly coccoid organisms in 100% of cases. This colonization was associated with loss of glycocalyx and clumping of the microvilli. The children with celiac disease (n = 9) all showed characteristic appearances with light microscopy, but only one had bacterial colonization on SEM. The surface features of specimens from children with other gastrointestinal disorders (food intolerance, postenteritis syndrome, protracted diarrhea of infancy, and immune deficiency states) were very similar to those from the CNSD group. Bacteria were visible on 89% of specimens, and in half of these cases the organisms were bacilli. SEM of specimens from children with no gastrointestinal disease (ages 11‐107 months) suggested an increased density of villi/unit area with advancing age. Bacteria were present in only two cases and did not include bacilli. The findings suggest that bacterial colonization of the surface of the small intestine is common in children with several gastrointestinal diseases and may play a part in their pathogenesis. Routine SEM examination of jejunal biopsies provides information not available from standard light microscopy, which may be relevant to the treatment of children with chronic diarrhea.