Research into the pathogenesis, prevention, and control of infectious and parasitic diseases remains a global priority as these scourges continue to be a substantial cause of mortality and morbidity. As highlighted in this Review Series, genome-wide approaches have provided great insight into a range of human pathogens, leading to greater understanding of the human diseases that they cause. Challenges that must be overcome in order to maximize our ability to use this wealth of genomic information are also discussed.