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Helicobacter pylori infection and iron and vitamin B12 deficiencies are widespread in economically disadvantaged populations. There is emerging evidence that H. pylori infection has a negative effect on the absorption of these micronutrients. The aim of this study was to evaluate the effect of H. pylori infection on the efficacy of micronutrient (including iron and vitamin B12)-fortified foods supplied for 1 year in marginally nourished children.In all, 543 Indian children, aged 6–10 years, participated in a double-blind, randomized controlled intervention trial, receiving foods fortified with either high (100% Recommended Dietary Allowances (RDA)) or low (15% RDA) amounts of iron, vitamin B12 and other micronutrients. The presence of H. pylori infection was diagnosed by the 13C-labeled urea breath test at 11 months after the start of the intervention. Blood hemoglobin, serum ferritin (SF), total body iron and plasma vitamin B12 were estimated at baseline and 12 months, and differences between these time points were assessed using an independent t-test.Overall, the prevalence of H. pylori infection in this group of children was 79%. Baseline hemoglobin, SF, body iron and vitamin B12 concentrations were not associated with H. pylori infection. The response to the intervention (either high or low amounts of iron and vitamin B12 fortification) in terms of change in iron markers and vitamin B12 status did not differ between children with and without H. pylori infection.This study shows that the presence of H. pylori infection did not affect the efficacy of long-term iron and vitamin B12 fortification in these marginally nourished children.