The purpose of this project is to build a prototype instrument that will, running unattended, detect, identify, and quantify BW agents. In order to accomplish this, we have chosen to start with the world's leading, proven assays for pathogens: surface-molecular recognition assays, such as antibody-based assays, implemented on a high-performance, identification (ID)-capable flow cytometer, and the polymerase chain reaction for nucleic-acid based assays. With these assays, we must integrate the capability to: (1) collect samples form aerosols, water, or surface; (2) perform sample preparation prior to the assays; (3) incubate the prepared samples, if necessary, for a period of time; (4) transport the prepared, incubated samples to the assays; (5) perform the assays; (6) interpret and report the result of the assays. Issues such as reliability, sensitivity and accuracy, quantify of consumables, maintenance schedule, etc. must be addressed satisfactorily to the end user. The highest possible sensitivity and specificity of the assay must be combined with no false alarms. Today, we have assays that can, in under 30 minutes, detect and identify simulants for BW agents at concentrations of a few hundred colony- forming units per ml of solution. If the bio-aerosol sampler of this system collects 1000 1/min and concentrates the respirable particles into 1 ml of solution with 70 percent processing efficiency over a period of 5 minutes, then this translates to a detection/ID capability of under 0.1 agent- containing particle/liter of air.