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31 patients of peptic ulcer (PU) treated in the past by vagotomy with Gastrojejunostomy (GJ)/pyloroplasty, later presented with dyspesia. These postvagotomy dyspeptic patients were investigated. Antral and corpus endoscopic biopsies were taken to evaluate for Helicobacter pylori (Hp) infection by inhouse rapid urease test (RUT), histopathological examination and scanning electron microscopy (SEM). Dyspepsia score was done in both pre and post treatment phase. Hp positive patients were randomised to receive anti H. pylori therapy. Hp eradication was recorded by repeat RUT and endoscopic biopsy followed by SEM. Coccoid form of Hp were detected in 76.92% cases of vagotomy with gastrojejunostomy (GJ) and coccobacillary forms of Hp were seen in 75% cases of pyloroplasty. After treatment with anti Hp therapy coccoid forms persisted in 69.23% of GJ cases, whereas 22% of pyloroplasty cases showed coccoid transformation. Anti Hp therapy did not reveal any statistically significant improvement in 'Dyspepsia Score' in GJ group, whereas it improved significantly in pyloroplasty group (p=0.002).