Although anemia in preschool children is most often attributed to iron deficiency, other nutritional, infectious, and genetic contributors are rarely concurrently measured. In a population-based, cross-sectional survey of 858 children 6–35 months of age in western Kenya, we measured hemoglobin, malaria, inflammation, sickle cell, α-thalassemia, iron deficiency, vitamin A deficiency, anthropometry, and socio-demographic characteristics. Anemia (Hb < 11 g/dL) and severe anemia (Hb < 7 g/dL) prevalence ratios (PRs) for each exposure were determined using multivariable modeling. Anemia (71.8%) and severe anemia (8.4%) were common. Characteristics most strongly associated with anemia were malaria (PR: 1.7; 95% confidence interval [CI] = 1.5–1.9), iron deficiency (1.3; 1.2–1.4), and homozygous α-thalassemia (1.3; 1.1–1.4). Characteristics associated with severe anemia were malaria (10.2; 3.5–29.3), inflammation (6.7; 2.3–19.4), and stunting (1.6; 1.0–2.4). Overall 16.8% of anemia cases were associated with malaria, 8.3% with iron deficiency, and 6.1% with inflammation. Interventions should address malaria, iron deficiency, and non-malarial infections to decrease the burden of anemia in this population.