To determine the prevalence of anaemia in children aged 6-24 months living in a high malaria transmission setting in Burundi, we used laboratory protocols to test anaemia using a portable hemocue analyser and screend for malaria using a Malaria Ag Pf/Pan rapid test; a rapid, qualitative test for the detection of HRP-II (Histidine rich protein II- HRP-2). We also detected Soil-Transmitted Helminthiasis and other faecal parasites microscopically by wet preparation and Kato-Katz technique. Laboratory protocols were used in cross-sectional that determined the prevalence and factors associated with anaemia in children aged 6-24 months living in a high malaria transmission setting in northern Burundi.