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Spatio-temporal variations in malaria burden are currently complex and costly to measure, but are important for decision-making. We measured the spatio-temporal variation of clinical malaria incidence at a fine scale in a cohort of children under five in an endemic area in rural Chikhwawa, Malawi, determined associated factors, and monitored adult mosquito abundance.

We followed-up 285 children aged 6–48 months with recorded geolocations, who were sampled in a rolling malaria indicator survey, for one year (2015–2016). Guardians were requested to take the children to a nearby health facility whenever ill, where health facility personnel were trained to record malaria test results and temperature on the child’s sick-visit card; artemisinin-based combination therapy was provided if indicated. The cards were collected and …