Over the past decade, the advent of genomics has facilitated the implementation of post-genomic strategies, including the application of new high-throughput technologies. Among the noticeable achievements is the protein microarray approach, a technology that is still in its infancy but that would greatly improve the diagnosis of bacterial pathogens. The present review summarizes the recent developments of this promising technique, including both antibody and protein microarrays. Several examples of the successful identification of infectious agents, such as Yersinia pestis, Bartonella and Tropheryma whipplei, are depicted. The multiplex detection, by protein microarrays, of several pathogens from a clinical sample is also discussed.