Deep sequencing was used to analyse Plasmodium falciparum DNA using blood samples from patients with malaria across Africa, Asia and Oceania. These data were used to develop a measurement of within-host parasite diversity that relates to the level of inbreeding and that is an important factor in the evolution of drug resistance. The data from this study are publicly available as a part of the ongoing MalariaGEN project, which aims to monitor evolutionary changes in this important pathogen.