Advances in microarray technology have allowed the identification of genetic variability over very long stretches of DNA in bacterial genomes [15] . These newly developed high density microarrays contain thousands to hundreds of thousands of oligonucleotide probes, instead of a few dozen, in a single array thereby expanding the power of identification [15] [16] [17] . In the current investigation we report the design and use of a high density oligonucleotide microarray for the identification of HAV and coxsackievirus (CV), both foodborne human pathogens. Our results indicate that the microarray hybridization technique can be applied to the identification of viruses of differing genus and species present in a sample and detect single nucleotide polymorphisms (SNP) to identify closely related viral strains belonging to the same species.