The correlation between clinical, serological, and endoscopic findings and histological response after a gluten-free diet (GFD) is limited in adult celiac (CD) patients. This study aims to evaluate the effects of GFD on intraepithelial lymphocyte (IEL) localization by comparing the histopathological, clinical, serological, and endoscopic findings of adult CD patients. The patients (n = 131) were divided into three groups: those with good (CDgc) (n = 23) and poor (CDpc) (n = 21) GFD compliance and newly diagnosed ones (nCD) (n = 87). Total and supranuclear IELs were counted per 100 enterocytes and divided into three groups: apical, mixed, and basal, according to ROC (Receiver operating characteristic) analysis. The roles of clinicopathological parameters in predicting good dietary compliance were calculated using the multivariable logistic regression model. CDgc group predominantly (78.3 %) exhibited a basal pattern, and none exhibited an apical. Conversely, most CDpc and nCD patients showed mixed (66.7 % and 73.6 %, respectively) and apical (9.5 % and 25.3 %) patterns. Non-atrophic Marsh types (p = 0.040) and basal pattern (p = 0.043) were independent parameters predicting good dietary compliance. This study first showed that IEL localizations can indicate GFD compliance in samples from CD patients. Localization-based examination of IELs can be an additional histological indicator in monitoring GFD compliance and signs of recovery, especially in adult CD patients.