To evaluate the use of intraepithelial lymphocyte (IEL) counts in identifying coeliac disease in childhood the jejunal histology from 116 children initially diagnosed as coeliac was reviewed. The diagnosis had been based on a characteristic mucosal abnormality and an apparent response to gluten exclusion. Lymphocyte counts were performed by one observer on the presenting biopsy and tissue samples obtained before and after a supervised gluten challenge. Results were expressed as IELs/100 enterocytes. On challenge 49% of patients failed to show histological deterioration with only one late relapse on 2 year follow-up. Reappraisal of these cases suggested alternate diagnoses, of which cow's milk protein intolerance (CMPI) (16%) and postenteritis malabsorption (20%) were the most common. In confirmed coeliacs IEL counts were high at diagnosis (67 +/- 16) (mean +/- SD), fell on diet (28 +/- 13), and rose on challenge (64 +/- 20). These changes were significant (p less than 0.01 using paired t test). Raised IEL counts at diagnosis were also found in patients with CMPI and giardiasis but a significant fall on diet only occurred in CMPI patients (p less than 0.05). Only patients showing mucosal relapse, i.e., confirmed coeliacs, showed a significant increase in IELs postgluten challenge compared with counts on a gluten-free diet. Although an increase in IELs showed good correlation with mucosal relapse on challenge, a high count at diagnosis was of insufficient specificity to obviate the need for gluten challenge.