The development of genomics has boosted research and our understanding of disease resistance in the model crop rice. While mapping and fine-mapping have been empowered by the release of thousands of new markers, this field of research is now entering a new era with the first examples of cloning genes by sequencing mutants. The few examples of genome wide association studies also indicate that identifying genes by this method will be challenging for minor effect loci. In all cases, phenotyping will be the key limitation to by-pass. The availability of large sets of genomic data also revealed several features of the defense system. While the polymorphism of genes upstream and downstream of the disease resistance pathway is mostly based on presence/absence, the polymorphism of genes in-between seems to rely more on expression level. Moreover, the different categories of genes involved in disease resistance are not evenly distributed in the genome. Altogether, the way this knowledge should modify our methods for breeding for disease resistance is discussed.