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Severely obese subjects have been found to show a high prevalence of distinct nutritional deficiencies even without any bariatric intervention but the underlying reasons remain obscure. We tested the hypothesis that gastric Helicobacter pylori infection is associated with increased nutritional deficiency rates. Taking advantage of our large database, we identified 404 patients who had undergone a gastroscopy--as a standard diagnostic assessment before bariatric surgery--along with a histological examination of gastric mucosal biopsies with concurrent nutritional blood measurements. Eighty-five (21 %) of the obese patients included in the study displayed a gastric H. pylori infection. Sex distribution, age and body mass index did not differ between H. pylori+ and H. pylori- patients (P > 0.29). Referring to nutritional markers, neither serum levels of total protein, albumin, calcium, phosphate, magnesium, ferritin, zinc, copper, vitamin B12, folate and 25-OH vitamin D3 nor respective deficiency rates differed between the H. pylori+ and H. pylori- patients group (all P > 0.13). Overall, 49.5 % of the bariatric candidates displayed at least one nutritional deficiency. Our data confirm previous reports on high prevalences of nutritional deficiencies in severely obese subjects. However, they do not provide evidence for a contributing role of gastric H. pylori infection to these nutritional alterations.