The National Institute of Allergy and Infectious Diseases (NIAID) has made a significant investment in genomics-related programs that provide comprehensive genome sequencing, transcriptomics, metagenomics, functional genomics, bioinformatics/databases, structural genomics, system biology and proteomics resources and reagents to the scientific community. The key components of the programs include the development of strong partnerships with the scientific community to respond rapidly to the community’s needs for genomic reagents and datasets, to support state-of-the-art technologies, to provide flexible resources to respond to public health emergencies, and to promote clear and consistent data- and reagent-sharing guidelines. New and emerging omics technologies, together with the integrated datasets that are generated, offer unprecedented opportunities for studying pathogens, their hosts, the environment and the microbiome and for developing novel and innovative strategies for the next generation of vaccines, drugs and diagnostics. These technologies have the potential to help control, treat and prevent infectious diseases around the globe.