Mucosal alterations after vertical banded Roux-en-Y gastric bypass have not been clearly evaluated. The aim of this paper was to analyze the histological findings and the presence of Helicobacter pylori in the excluded stomach. Forty consecutive patients who underwent Roux-en-Y gastric bypass longer than 36 months were selected for double-balloon enteroscopy. The excluded stomach was reached in 35/40 patients (88%). Morphological alterations were analyzed through hematoxilin and eosin and the presence of H. pylori was confirmed with Giemsa staining. Thirty patients (86%) were female, and the mean age was 43 years old. The mean postoperative time was 78 months (36-110 months). Histologically, all patients had chronic gastritis in the bypassed stomach, with pangastritis in 33/35 (94%). Five cases (5/35, 14%) presented atrophy and four of them also had intestinal metaplasia. Helicobacter pylori was detected in 7/35 (20%) of the excluded stomach and in 12/35 (34%) of the functional pouch. All patients positive for H. pylori in the excluded stomach were also positive in the functional pouch, p = 0.0005. Helicobacter pylori is still present in the excluded stomach after Roux-en-Y gastric bypass and might be considered for treatment. Histological findings indicated high prevalence of atrophy and intestinal metaplasia in this selected population.