The chicken has led the way among agricultural animal species in infectious disease control and, in particular, selection for genetic resistance. The generation of the chicken genome sequence and the availability of other empowering tools and resources greatly enhance the ability to select for enhanced disease resistance via genetic markers and to understand more deeply the biological basis of host resistance. In this review, we discuss how integrated genomic approaches are able to identify specific genes and genetic markers associated with disease resistance, give select examples of contemporary work involving various genomic strategies to identify disease resistance genes, and finish by giving some final thoughts on predicted applications in the near future.