Several experimental studies have demonstrated that activated intestinal T cells can induce villous atrophy. This observation led us to examine the possible role of activated T cells in the pathogenesis of intestinal lesions in a group of 13 children with intractable diarrhea and villous atrophy of unknown origin. Immunohistochemical study showed signs of intestinal mononuclear cell activation in seven patients. These signs included a marked increase in the number of mucosal T cells, mainly TCR alpha beta+, the appearance of lamina propria interleukin-2-receptor-bearing cells, and an increased expression of HLA-DR antigens by enterocytes. No local cause of intestinal T-cell activation was found. However, four out of seven patients had extradigestive symptoms of autoimmunity, suggesting that the intestine might also be the site of an autoimmune reaction responsible for the epithelial lesions. In these patients, presence of crypt necrosis and colic extension of the lesions suggested poor prognosis. In contrast, in six other patients, no immunohistochemical evidence of mucosal T-cell activation was obtained. In the latter cases, analysis of clinical data favored the hypothesis of a primary inborn defect of enterocyte differentiation.