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Malaria-causing parasites display remarkable cellular plasticity during their complex life cycle, but remain relatively uncharacterized at the molecular level. Here, Howick et al. use a modified Smart-seq2 approach, to profile the single-cell transcriptomes of thousands of individual malaria parasites, spanning the entire life-cycle of Plasmodium berghei. Droplet sequencing was applied to further characterize cells from red blood cell stages of P. berghei and three additional species, P. falciparum, P. malariae and P. knowlesi, including parasites taken from patients with malaria. The resulting freely accessible data set, the Malaria Cell Atlas, provides insight into gene usage and function, and may inform future drug and vaccine development.