Aims: The Cepheid GeneXpert (R) is a four-site, automated sample preparation and real-time PCR detection system. In this study, the capability of the GelleXpert (R) to isolate and detect nucleic acid from Bacillus anthracis Allies spores was assessed. Methods and Results: A four-plex, dried-clown bead cartridge containing PCR reagents specific for the pXO1 and pXO2 plasmids as well as sample processing and inhibition controls was evaluated. For B. anthracis Ames spores harbouring pXO1 and pXO2, samples containing 68 CFU per ml (148 spores per ml) were positive in all four replicates. A limited cross-reactivity panel, which included closely related Bacillus species, was also tested to determine the specificity of the pXO1 and pXO2 assays. No cross-reactivity occurred. Further, B. anthracis Sterne spore samples were analysed to compare results when processed using the GeneXpert (R) to those run directly oil the Cepheid SmartCycler (R) without sample processing. The GeneXpert (R) detection capability was three logs lower than the SmartCycler (R) indicating the benefit of incorporating a nucleic acid extraction procedure. Conclusions: This study demonstrates that the GeneXpert (R) is a rapid and reliable system for simultaneously detecting the B. anthracis virulence plasmids pXO1 and pXO2. Significance and Impact of the Study: The GeneXpert (R) is the only platform currently available that is capable of both nucleic acid purification and real-time PCR detection enclosed within a single system. Further, all sample manipulations are automated, thus reducing errors associated with manual processing.