The current explosion in new high-throughput technologies arising from microbial and animal genomics studies is enabling the analysis of the genome, transcriptome, and proteome and offers the opportunity to gain a better understanding of the molecular pathways underlying pathogen biology, the host immune system, and host-pathogen interactions. These new tools can be applied to veterinary pathogens to overcome some of the current hurdles in the discovery of highly effective vaccines for farmed livestock and poultry.