One of the ways to take advantage of proteome arrays from infectious microorganisms is in the area of vaccine antigen discovery and vaccine development. Our “Agile” vaccine development pathway, is intended to accelerate the discovery and deployment of safe and effective vaccines. One of the most difficult tasks in developing a recombinant protein subunit vaccine or DNA vaccine is the identification of the antigens that will stimulate the most effective immune response against the pathogen, particularly when the genome of the organism is large. A comprehensive way to accomplish this would be to obtain each of the structural, metabolic, and regulatory antigens of the pathogen and test their protective immunity individually or as mixtures in the vaccine. Although this approach may work for small viruses encoding several antigens, it is not practical for large viruses like smallpox or bacteria which encode 100s or thousands of antigens. In response to this challenge, our laboratory has developed PCR Express to rapidly generate plasmids that can be expressed in an in vitro transcription/translation system. The resulting proteins are spotted onto microarray chips, and the chips are used to monitor serum antibody titers from vaccinated or infected, humans and animals. This analysis can comprehensively scan entire microorganism proteomes and identify those antigens that are recognized by the immune system following vaccination or infection. This empirical data set can be combined with bioinformatics approaches to select superior vaccine antigen targets. Our experience is that this empirical analysis leads to the identification of a manageable subset of antigens, and our expectation is that for each infectious agent several antigens will be administered together in the vaccine. We are currently supported to use this approach to identify the vaccine antigen sets for smallpox, F. tularensis, P. falciparum (malaria), and B. pseudomallei, and we are accumulating proof that the approach is effective.