Regional iron concentrations in the brains of children with Sickle Cell Anaemia (SCA) were examined using susceptibility mapping (SM), in the first study to apply SM to an African cohort in Tanzania. Mean susceptibility values in three deep-brain regions were compared to age, blood ferritin levels and history of clinical stroke. Mean susceptibility values increased linearly with age, but there was no significant correlation between susceptibility values and blood ferritin levels. SCA patients who had suffered stroke prior to MRI had significantly lower susceptibility values than stroke-free patients. This may suggest a role for iron deficiency in stroke in SCA.