Asymptomatic malaria parasitaemia is prevalent among schoolchildren in many countries. The relationship between asymptomatic parasitaemia and children's cognitive functions was examined in a case control study and then in a natural experiment. A group (n = 445) of asymptomatic parasitaemic boys were compared with a group of non-parasitaemic boys (n = 142) matched for grade and school on their performance on a battery of cognitive tests. Two weeks later the parasitaemic children were re-screened and 150 children of those who remained parasitaemic were matched for grade and school with 150 children who were no longer parasitaemic. These children were then re-tested and their cognitive function compared. Initially, after controlling for age, socio-economic background and nutritional status the parasitaemic children performed worse than the non-parasitaemic children in fine motor function tests. There was no difference in change in cognitive test scores between those who became non-parasitaemic and those who remained parasitaemic. However, children who initially had the highest parasite density improved the most in 2 fine motor tests and a picture memory test. We were unable to show a benefit from losing parasitaemia over a 2 week period, but it remains possible that parasitaemia may affect cognition and longer term trials should be conducted.