Microarray technology has revolutionized the detection and analysis of microbial pathogens. The success of this technology is evident from the various microarrays that have been developed for this purpose, variation in the density of probes, and the time ranges required for assay completion. Among these, high-density re-sequencing microarrays have demonstrated great potential for detecting bacterial, viral pathogens, and virulence markers. Resequencing microarrays use closely overlapping probe sets to determine a target organism's nucleotide sequence. Hybridization to a series of perfect matched probes provides confirmatory presence/absence information, while hybridization to mismatched probes reveals strain-specific single nucleotide polymorphism (SNP) data. This approach provides sequence information of the diagnostic regions of detected organisms that is considerably more informative over that provided from other microarray techniques.