This chapter will explore the ways in which genomics (and the informatics tools needed to analyze and interpret them) could, potentially, transform our understanding of infectious disease epidemiology, improve disease management and prevention and save lives. The integration of microbiological, clinical and environmental data into personalized clinical decision support and risk assessment tools will improve both the care of patients with infectious diseases and public health protection. Integrated electronic health information systems will be faster, safer and more cost-effective than the current inefficient miscellany of individual medical records and disease surveillance systems. Technical, commercial and economic barriers to system implementation are unlikely to be insurmountable, but the largely uncharted ethical hazards are potentially more challenging. Prospective evaluation of clinical and public health impact and cost-effectiveness of new diagnostic and surveillance methods and information systems, designed to protect privacy and security of health data without placing unnecessary restrictions on access to essential public health data, will be needed. The interests, priorities and concerns of all stakeholders, including patients and potential patients, health professionals and administrators, public health officials and politicians, must be openly debated and addressed. Otherwise, unnecessary delays or a failure to implement better systems will allow unnecessary suffering and preventable mortality to continue.