Within the past dozen years, outbreaks of filoviral hemorrhagic fever within the human population have been occurring with increasing frequency, with an average of 1 epidemic now occurring every 1-2 years. Many of the outbreaks have been large (involving >150 cases), necessitating rapid responses from the international community to help implement infection control and surveillance. This increased activity, combined with today's climate of bioterrorism threats, has heightened the need for high-throughput methodologies for specific detection of these high-hazard viruses in sophisticated laboratory setups and mobile field laboratory situations. Using Zaire Ebola virus as an example, we describe here the development of a high-throughput protocol for RNA extraction and quantitative reverse-transcription polymerase chain reaction analysis that is safe, fast, and reliable. Furthermore, the applicability of this method to an outbreak setting was demonstrated by correct analysis of >500 specimens at a field laboratory established during a recent outbreak of Marburg hemorrhagic fever in Angola.