A morphometric and immunohistochemical restudy was made of jejunal biopsy specimens from 5 patients with soy allergy and the results obtained were compared to those from specimens taken before soy feeding and to those at a later time. All the patients had had previous cow's milk allergy with malabsorption. Gastrointestinal symptoms presented within two weeks of starting the soy based formula but in two patients the symptoms were mild and these patients were able to continue soy feeding. Jejunal biopsy specimens taken within 3 days from the reaction to soy showed villous atrophy associated with crypt hyperplasia and an increased cell renewal rate. Also, these specimens showed an inflammatory reaction in the lamina propria and in the epithelium, and the numbers of IgA- and IgM-containing cells were increased. Later, when the soy proteins were eliminated, the morphology of the jejunum improved and the cell numbers were reduced to normal. The intestinal damage and the local immune reaction caused by soy proteins are similar to those seen in cow's milk allergy with malabsorption. The immunological mechanisms operating in these diseases are thought to be the cause of these changes.