In sub-Saharan Africa iron deficiency and malaria are the major causes of anaemia in children under five years of age. Assessment of iron deficiency, using biochemical iron markers in areas of high malaria transmission and infection can be difficult as markers are altered by the acute phase response. Results of the ‘gold standard’ test used to diagnose iron deficiency, namely bone marrow iron microscopy, has also occasionally been inconsistent. This monograph describes findings from a study aimed at evaluating methods of assessing iron deficiency in the bone marrow and peripheral blood, and investigating the association between iron deficiency and infection in children living in a malaria endemic area. This monograph is for research scientists who are interested in unravelling the complex story of iron and infection.