It has been suggested that in doubtful cases of coeliac disease, a high CD3+ T-cell receptor gamma delta+ (TCRγδ+) intraepithelial lymphocyte count increases the likelihood of coeliac disease. Aim: To evaluate the diagnostic accuracy of both an isolated increase of TCRγδ+ cells and a coeliac lymphogram (increase of TCRγδ+ plus decrease of CD3− intraepithelial lymphocytes) evaluated by flow cytometry in the diagnosis of coeliac disease. Methods: The literature search was conducted in MEDLINE and EMBASE. The inclusion criteria were: an article that allows for the construction of a 2 × 2 table of true and false positive and true and false negative values. A diagnostic accuracy test meta-analysis was performed. Results: The search provided 49 relevant citations, of which 6 were selected for the analysis, which represented 519 patients and 440 controls. Coeliac lymphogram: The pooled S and Sp were 93% and 98%, without heterogeneity. The area under the SROC curve (AUC) was 0.98 (95% CI, 0.97–0.99). TCRγδ+: Pooled S and Sp were both 95%, with significant heterogeneity. The AUC was 0.97 (95% CI, 0.95–0.98). Conclusions: Both TCRγδ+ count and coeliac lymphogram assessed by flow cytometry in duodenal mucosal samples are associated with a high level of diagnostic accuracy for and against coeliac disease.