The prevalence of malnutrition in Cambodia is among the highest in Southeast Asia, and diarrhea and pneumonia are the leading causes of death among children. Whether these adverse health outcomes are associated with co-existing micronutrient deficiencies is uncertain. We have determined the prevalence of anaemia, as well as iron, zinc, and vitamin A deficiency and their co-existence among stunted children (77 females; 110 males) aged 6-36 mos. Non-fasting morning venipuncture blood samples were taken and analyzed for haemoglobin (Hb), serum ferritin (via IMx system), retinol (via HPLC), and Zn (via AAS), C-reactive protein (CRP) (via turbidimetry) and Hb type (AA, AE, or EE) (via Hb gel electrophoresis). Children with CRP>or=5.0 mg/L (n=34) were excluded. Zinc deficiency defined as serum Zn<9.9 micromol/L had the highest prevalence (73.2%), followed by anaemia (71%) (Hb<110 g/L), and then vitamin A deficiency (28.4%) (serum retinol<0.70 micromol/L). Of the anaemic children, only 21% had iron deficiency anaemia, and 6% had depleted iron stores. Age, log serum ferritin, and Hb type were significant predictors of Hb in the AA and AE children. Serum retinol was unrelated to haemoglobin or serum zinc. The prevalence of two or more micronutrient deficiencies (low Hb, serum retinol, and/or serum zinc) was 44%. Nearly 10% had low values for all three indices, and 18% had just one low value. In conclusion, anaemia, and deficiencies of iron, zinc, and vitamin A are severe public health problems among these stunted Cambodian children. Intervention strategies addressing multiple micronutrient deficiencies are needed.