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Helicobacter pylori causes a chronic gastric infection, which is usually life-long. Many epidemiological studies have shown that this is probably one of the most common bacterial infections throughout the world involving 30% of the population living in developed countries and up to 80–90% of the population in developing regions. Concomitantly, developing regions also have high prevalence of micronutrient malnutrition. In the last few years, some studies have suggested that H. pylori infection may affect the homeostasis of different micronutrients including iron, vitamin B12, folic acid, α-tocopherol, vitamin C and β-carotene. In this article, we discuss the current scientific information of the effect that H. pylori infection may produce on micronutrient malnutrition.