The prevalence of anemia in Aboriginal children is high, but, given the high burden of infection in these children, the extent to which anemia is due to iron deficiency and/or infection is unclear. To determine the contribution of iron deficiency to anemia, we screened 144 Aboriginal infants (70 boys, 74 girls) who were free from infection. The prevalence of anemia (hemoglobin <105 g/L) was 18.8%; caregivers reported that 53.5% of infants had had an infection in the two weeks before screening. Anemic infants were more likely than non-anemic infants to have had an infection before screening (74.1% versus 48.7%, p = 0.02), and anemic infants had a higher prevalence of iron deficiency revealed by low serum iron concentrations (<7 micromol/L) (73.7% versus 38.3%, p <0.01). Iron deficiency measured using serum ferritin concentration tended to be less marked in infants who had had an infection (13% versus 30.3%, p = 0.06); this is probably because serum ferritin is a positive acute-phase protein. This study indicates the difficulty of isolating the contribution of infection to anemia from the separate effects of dietary iron deficiency.