This cross-sectional population-based study investigated prevalence rates and associated factors for anemia, iron deficiency anemia, and iron deficiency among children 6 to 60 months of age in two towns in Acre State, Brazil (N = 624). Hemoglobin, plasma ferritin, and soluble transferrin receptor were measured in venous blood samples. Socioeconomic, demographic, and disease data were obtained using a questionnaire. Prevalence ratios were calculated by Poisson regression in a hierarchical model. Prevalence rates for anemia, iron deficiency anemia, and iron deficiency were 30.6%, 20.9%, and 43.5%, respectively. Children younger than 24 months showed higher risk of anemia, iron deficiency anemia, and iron deficiency. The highest family income tertile was a protective factor against iron deficiency anemia (PR: 0.62; 95%CI: 0.40-0.98). The highest height-for-age quartile was protective against anemia (0.62; 0.44-0.86) and iron deficiency anemia (0.51; 0.33-0.79), and recent history of diarrhea was associated with increased risk of anemia (1.47; 1.12-1.92) and iron deficiency anemia (1.44; 1.03-2.01). Geohelminth infection was associated with increased risk of anemia, iron deficiency anemia, and iron deficiency.