The need for partial gastrectomy has decreased as a result of reduced incidence and improved endoscopic and medical treatment of peptic ulcer disease. Nonetheless, several patients with resected stomach remain in the population, and it is well known that important pathological changes can occur in the gastric remnant. We evaluated the morphological and functional status of the gastric stump by use of modified endoscopic Congo red test (MCRT). For this purpose, 87 partially gastrectomized (Billroth I and II) patients referred for elective gastroscopy were consecutively enrolled. We found a high prevalence of severe chronic atrophic fundal gastritis (CAFG) (67%) in the gastric remnant. We also observed, however, that one-third of the patients had almost unaffected gastric acid production even as long as 26 years after partial gastrectomy. Moreover, the accuracy, sensitivity, and specificity of routine gastroscopy in diagnosing CAFG in the gastric stump were found to be 55%, 50%, and 84%, respectively. The presence of bile reflux correlated well with the degree of CAFG. Importantly, we observed that more than 71% of the patients receiving acid-suppressing therapy had no or very little capacity to produce gastric acid. Taken together, our study has demonstrated that MCRT is a simple and well-tolerated method providing important morphological and functional information about the mucosa of the resected stomach. Furthermore, MCRT was superior to routine gastroscopy in diagnosing CAFG in the gastric stump. Outcome studies should define the clinical benefit of MCRT in the management of patients with resected stomach.