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Background: Anemia is common among children in Aboriginal communities in Canada. The objectives of this study were to determine the prevalence of anemia and to identify its associated risk factors among young children in Aboriginal communities in northern Ontario and Nunavut., Methods: 115 children from one Inuit and two Cree First Nations communities participated. We collected information on demographic and dietary factors and measured hemoglobin (Hb), ferritin (SF), serum transferrin receptor (sTfR) and Helicobacter pylori IgG antibodies. Odds ratios and 95% confidence intervals were determined to examine risk factors associated with anemia and iron deficiency (ID) and further analyzed using stepwise regression procedures., Results: Prevalence of anemia (Hb<110 g/L) was 36.0%. Iron deficiency (sTfR>8.5 mg/L) was present in 27.6% of the study population. Approximately 53.3% had depleted iron stores (SF<12 microg/L). Consumption of cow/evaporated milk was the only independent risk factor associated with anemia. Infection with H. pylori and prolonged consumption of breastmilk were also associated, although not independently, with anemia. Formula intake was negatively associated with ID., Interpretation: The prevalence of anemia in Aboriginal children was eight times higher than among similar populations in urban Canada and was especially high among Inuit children. ID was the major cause of anemia, but not the only one, since 10% of anemic children were not iron deficient. Given that the consumption of cow/evaporated milk was found to be a significant independent risk factor associated with anemia, public health strategies should include promotion of breastfeeding, combined with iron-rich complementary foods, while addressing socio-economic conditions that may be preventing these practices from being adopted. H. pylori may be a major contributing factor to anemia, thus improvements in water quality and sanitation also need to be considered.