BACKGROUND:Malaria and anaemia (Haemoglobin= 11 g/dl. For each participant, a physical examination was done and anthropometric data collected prior to a biological assessment which included: malaria parasitaemia infection, intestinal worm carriage, G6PD deficiency, sickle cell disorders, and alpha-talassaemia.RESULTS:Three hundred and fifty two children 5 years (aOR=0.03, 95%CI0.01-0.08]). Stratified by age group, anaemia was significantly associated with stunting in children less than 5 years (aOR=3.1 95%CI1.4 -- 6.8]), with, sickle cell disorders (aOR=3.5 95%CI 1.4 -- 9.0]), alpha-thalassemia (or=2.4 95%CI1.1--5.3]) and stunting (aOR=3.6 95%CI 1.6--8.2]) for children above 5 years. No association was found between G6PD deficiency, intestinal worm carriage and children's gender.CONCLUSION:Malaria parasitaemia, stunting and haemoglobin genetic disorders represented the major causes of anaemia among study participants. Anaemia control in this area could be achieved by developing integrated interventions targeting both malaria and malnutrition.