The COVID-19 pandemic has revealed the need for nations to prepare more effectively for emerging infectious diseases. Preparing for these threats requires a multifaceted approach that includes assessing pathogen threat, building flexible capabilities for rapid medical countermeasure (MCM) development, and exercising, maintaining, and improving those response capabilities. The Biomedical Advanced Research and Development Authority (BARDA) promotes the advanced development of MCMs in response to natural and manmade threats. In this article, the authors describe a BARDA threat assessment tool that, in conjunction with other factors, facilitates portfolio management and decisionmaking related to the advanced development of MCMs for emerging infectious diseases. The tool was designed to use readily accessible public data and information related to the threat posed by pathogens. It can be adjusted to modify the specific areas of interest (eg, removal/addition of parameters) to facilitate cross-pathogen analysis and can be updated to reflect changes (eg, new outbreak) that may impact the overall threat assessment. Finally, assessment of certain pathogens is included.