BACKGROUND: Helicobacter pylori infection treatment was found not to reduce the prevalence of iron deficiency or anemia among Alaska Native children at 14 months after treatment initiation. We hypothesized that 14 months was to early to resolve H. pylori-induced gastric damage. Consequently, we conducted a 40-month follow-up. METHODS: We enrolled 219 children 7-11 years old who had H. pylori infection (as diagnosed by (13)C-labeled urea breath test) and iron deficiency (serum ferritin level, 14 months modestly reduced the prevalence of iron deficiency and substantially reduced the prevalence of iron deficiency and anemia. H. pylori likely plays a casual role in hematological outcomes for some children.