Objective Bile reflux is thought to be responsible for reflux gastritis and stump carcinoma occurring after partial gastrectomy for peptic ulcer. Gastritis and gastric carcinoma are also correlated with Helicobacter pylori. The aim of this study was to investigate whether diversion of enteric reflux and the presence of H. pylori infection alter long-term histological developments in the gastric remnant. Methods Twenty-nine patients partially gastrectomized for peptic ulcer were reoperated on with re-resection and a Roux-en-Y reconstruction because of reflux gastritis (12 patients) or severe dysplasia/early gastric cancer (17 patients). The resected specimens and subsequent biopsies from the new anastomotic region taken at endoscopies 5-17 years after reoperation were evaluated regarding the presence of H. pylori, the grade of active and non-active chronic gastritis, and the premalignant changes - atrophy, intestinal metaplasia and dysplasia. Results A progression of active chronic gastritis, atrophy, intestinal metaplasia and dysplasia was seen after re-resection and Roux-en-Y reconstruction. Non-active chronic gastritis remained unchanged. The development was, in general, independent of H. pylori infection. Conclusions Enteric reflux may perhaps induce a histological transformation of the gastric mucosa that cannot be reversed, even if the reflux is diverted. In our study, H. pylori infection had no impact on the histological development. Factors other than enteric reflux and H. pylori infection might also be of importance.