OBJECTIVES: Gastroesophageal reflux disease (GERD)-associated changes in esophageal histology have been reported mainly after short-term medical antireflux therapy, and few individual lesions have been examined. We report detailed histological findings from the LOTUS study, at baseline and at 1 and 3 years after laparoscopic antireflux surgery (LARS) or esomeprazole treatment in patients with chronic GERD. METHODS: LOTUS is a long-term, open, parallel-group, multicenter, randomized, controlled trial conducted in 11 European countries that compared LARS (n=248) with esomeprazole 20-40 mg daily (n=266). Biopsies from the distal esophagus 2 cm above the Z-line and at the Z-line were taken at baseline, and 1 and 3 years. The following lesions were assessed: basal cell hyperplasia (BCH), papillary elongation (PE), intercellular space dilatations (ISDs), intraepithelial eosinophils (EOSs), neutrophils, and necrosis/erosion. A severity score (SS, range 0-2) was calculated by taking the average score of all assessable lesions. RESULTS: All lesions were more severe on Z-line biopsies than at 2 cm, and almost all improved significantly from baseline to 1 and 3 years. The average SS (from 2 cm to Z-line) changed from 0.95 to 0.57 (1 year) and to 0.49 (3 years) on esomeprazole, and from 0.91 to 0.56 (1 year) and to 0.52 (3 years) after LARS (P<0.001 for both treatments at 1 and 3 years, with no significant difference between treatments). The proportions of patients with severe histological changes decreased from approximately 50% at baseline to 11% at 3 years. CONCLUSIONS: Both continuous esomeprazole treatment and laparoscopic fundoplication are associated with significant and similar overall improvement in microscopic esophagitis after 1 year that is maintained at 3 years.