Patients with non-erosive reflux disease may show microscopic damage. This study is aimed to describe distribution, sensitivity, and specificity of histological lesions (i.e., basal cell hyperplasia-BH, papillae elongation-PE, dilatation of intercellular spaces-DIS, intraepithelial eosinophils-IE, neutrophils, and erosions) and sampling criteria. Four groups were identified on the basis of symptoms, endoscopy, and pH monitoring: (1) erosive esophagitis (n = 48), (2) non-erosive esophagitis with abnormal pH (n = 59), (3) non-erosive esophagitis with normal pH (n = 12), and (4) controls (n = 20). Biopsies were taken at the Z-line and 2 and 4 cm above it. BH, PE, DIS, IE, neutrophils, and erosions were assessed. A global severity score was calculated on the basis of the above parameters and allowed the distinction of patients from controls with 80% sensitivity and 85% specificity. Lesions were more severe at Z-line than proximally and more expressed in erosive than in non-erosive disease, although more than 70% of latter patients still showed histological damage. Esophageal biopsy seems very attractive in non-erosive disease where it may contribute to diagnosis and play a role in the comparative evaluation of different therapies.