This article describes the results of the human immunodeficiency virus (HIV) and sexually transmitted infections (STI) prevention in the emergency department (ED) component of the 2009 Academic Emergency Medicine Consensus Conference entitled “Public Health in the ED: Surveillance, Screening, and Intervention.” The objectives were to use experts to define knowledge gaps and priority research questions related to the performance of HIV and STI surveillance, screening, and intervention in the ED. A four-step nominal group technique was applied using national and international experts in HIV and STI prevention. Using electronic mail, an in-person meeting, and a Web-based survey, specific knowledge gaps and research questions were identified and prioritized. Through two rounds of nomination and refinement, followed by two rounds of election, consensus was achieved for 11 knowledge gaps and 14 research questions related to HIV and STI prevention in EDs. The overarching themes of the research priority questions were related to effectiveness, sustainability, and integration. While the knowledge gaps appear disparate from one another, they are related to the research priority questions identified. Using a consensus approach, we developed a set of priorities for future research related to HIV and STI prevention in the ED. These priorities have the potential to improve future clinical and health services research and extramural funding in this important public health sector.