In Cambodia, many factors may complicate the detection of iron deficiency. In a cross-sectional survey, we assessed the role of genetic hemoglobin (Hb) disorders, iron deficiency, vitamin A deficiency, infections, and other factors on Hb in young Cambodian children. Data on sociodemographic status, morbidity, and growth were collected from children (n = 3124) aged 6 to 59 mo selected from 3 rural provinces and Phnom Penh municipality. Blood samples were collected (n = 2695) for complete blood count, Hb type (by DNA analysis), ferritin, soluble transferrin receptor (sTfR), retinol-binding protein (RBP), C-reactive protein, and α(1)-acid glycoprotein (AGP). Genetic Hb disorders, anemia, and vitamin A deficiency were more common in rural than in urban provinces (P < 0.001): 60.0 vs. 40.0%, 58.2 vs. 32.7%, and 7.4 vs. 3.1%, respectively. Major determinants of Hb were age group, Hb type, ferritin, sTfR, RBP, AGP >1.0 g/L (P < 0.001), and rural setting (P < 0.05). Age group, Hb type, RBP, elevated AGP, and rural setting also influenced ferritin and sTfR (P < 0.02). Multiple factors affected anemia status, including the following: age groups 6-11.99 mo (OR: 6.1; 95% CI: 4.3, 8.7) and 12-23.99 mo (OR: 2.7; 95% CI: 2.1, 3.6); Hb type, notably Hb EE (OR: 18.5; 95% CI: 8.5, 40.4); low ferritin (OR: 3.2; 95% CI: 2.2, 4.7); elevated AGP (OR: 1.4; 95% CI: 1.2,1.7); rural setting (OR: 2.3; 95% CI: 1.7, 3.1); low RBP (OR: 3.6; 95% CI: 2.2, 5.9); and elevated sTfR (OR: 2.1; 95% CI: 1.7, 2.7). In Cambodia, where a high prevalence of genetic Hb disorders exists, ferritin and sTfR are of limited use for assessing the prevalence of iron deficiency. New low-cost methods for detecting genetic Hb disorders are urgently required.