Clinically significant gluten-sensitive enteropathy (GSE) can be associated with architecturally normal small bowel villi and evenly distributed increased intraepithelial T lymphocytes (IELs). This distribution pattern of IELs has been shown to be a sensitive feature of GSE but to be of relatively low specificity, thus limiting its usage as a diagnostic marker. We demonstrate herein the potential diagnostic role of IEL immunophenotyping. We show that a top-heavy distribution pattern of CD3+ IELs is a sensitive diagnostic feature of GSE. Despite overlap between GSE and non-GSE patients, the difference is underscored when using a tip-to-base ratio. Of the GSE patients, 87.5% showed a tip-to-base ratio >1.7 compared with only 12.5% of non-GSE patients and none in controls. This pattern was retained in 50% of treated GSE patients, although the CD3+ tip-IEL scores were significantly smaller. Conversely, CD8 immunostaining appears of limited diagnostic value. The discrepancy in distribution of CD3+ and CD8+ IELs between GSE and non-GSE patients can be explained by the presence of CD4- CD8- TCR-gamma delta+ IELs which, have been reported in GSE. Since the immunophenotyping of T- IELs is feasible with readily available antibodies, and given the clinical benefits for patients with 'latent' GSE, we advocate using CD3 immunostaining to triage patients with normal villi and increased IELs.