In this study we have compared the results of Scanning Electron Microscopy (SEM) with Light- and Stereomicroscopy in a series of small bowel biopsies in children. In 9 cases displaying features of partial or subtotal atrophy, Light and Dissecting-Microscopy yielded similar results. The distinction between coeliac and non-coeliac chronic diarrhoea was only possible on clinical grounds, and by the immunological detection of specific antibodies. On SEM however coeliac patients showed characteristic alterations consisting of: absence of villi; prominent crypt outlets resulting in a mosaic appearance; concentric furrows running all around the openings; and downy brush feature at high power. The microvilli were loosely distributed and had an irregular pleomorphic outline; they often displayed a drumstick swelling of the tip and were bent. In contrast, non-coeliac chronic diarrhoea cases were characterized by a thick mucous layer on the mucosal surface, that made it impossible to visualize further changes. Peculiar vascular changes in lymphangiectasia and in sickle beta thalassemia could be detected only by Light Microscopy. In addition, in the lymphangiectasia case SEM allowed the detection of enteroadherent bacteria; and in the lambliasis case, of pseudomembranes. Absence of glycocalyx was noted both in controls and in patients. The results of this study point to a diagnostic utility of SEM particularly in the differential diagnosis of chronic diarrhoea; moreover they suggest that enteroadherent bacteria may not be pathogenic and that the absence of glycocalyx is not specific for allergic enteropathy as previously claimed.