The US Department of Homeland Security finished its first bioterrorism risk assessment in January 2006. That and the upcoming 2008 assessment employs a probabilistic risk assessment methodology designed to guide prioritization of ongoing biodefense-related research, development, planning and preparedness. The methodology and the scientific work it subsequently identifies as necessary have generated some discussion about both its design and consequence. This paper clarifies the current debate, describes the current processes in place, and identifies issues that merit further discussion.