The appearance of the small intestinal mucosa in cow's milk protein intolerance (CMPI) was studied using quantitative morphometry. The parameters under study were the numbers of eosinophil cells in the lamina propria and epithelium, villous height, crypt zone depth, villous height/crypt zone depth ratio, and total mucosal thickness. Tracings of whole sections were analysed using a suitably programmed minicomputer linked to a digitising table. Small bowel biopsy specimens from children with untreated CMPI, from children before and after clinical relapse on cow's milk challenges, and from children with resolved CMPI were compared to each other, to those from control infants, and to those from children with coeliac disease. No change of diagnostic significance could be found in the number of lamina propria eosinophil cells, but levels of intraepithelial eosinophils were significantly increased following cow's milk challenge. Quantification of mucosal dimensions confirmed the presence of a cow's milk-sensitive enteropathy and established the finding of a thin mucosa in CMPI regardless of clinical disease activity. Mucosal thickness was not different from control values following resolution of the disease. In coeliac disease mucosal thickness was significantly greater than in CMPI (apart from young children with untreated coeliac disease whose mucosa was not thicker than that of children with untreated CMPI) but not different from control values. It is suggested that in CMPI there is a limitation in the capacity of crypt cells to compensate for the loss of villous epithelium.