A new method has been developed to analyse intra-host genetic diversity of malaria infections from patient blood. Malaria infections are often comprised of a complex assortment of parasite lineages — also known as multiple-genotype infections. In this study, cell sorting was followed by whole-genome amplification to generate sufficient DNA from infected red blood cells for subsequent genotyping and sequencing analyses. Better understanding the impact of various combinations of intra-host drug resistance and virulence haplotypes could facilitate more directed treatment strategies in the future.