Health is one of the most important contributors to animal welfare, productivity and profitability in pig production today. For the past 30 years, pig breeders have focused on genetic improvement of lean growth, feed efficiency, meat quality and reproduction. However, in recent years, selection objectives have been broadened to include livability, robustness and disease resistance. A DNA marker for selection of resistance to F18+ E. coli has been available for several years. This marker decreases mortality and improves growth on farms experiencing post-weaning scours and/or oedema disease. However, for most diseases affecting intensive production systems such as porcine reproductive and respiratory syndrome (PRRS), porcine circovirus type 2-associated diseases (PCVAD), Haemophilus parasuis, and swine influenza virus, resistance is a complex and polygenic trait. Selection for improved resistance to these diseases will be incremental and require use of multiple markers in complex breeding schemes. Novel technologies such as pig gene microarrays, single nucleotide polymorphism (SNP) panels and advanced bioinformatics are being used to identify new health candidate genes for these economically important diseases. Lagging behind, however, is availability of large DNA datasets from pedigreed populations with accurately measured health phenotypes that are needed to identify associations between SNPs and health traits. Increased focus on datasets with health traits will be the key to finding useable discoveries with new genomics technologies. Currently, the industry uses dozens of SNP markers to increase the accuracy of selection for complex breeding objectives, including disease resistance. As the pig genome is sequenced and barriers to genotyping thousand of markers are eliminated, genomic selection for health traits will receive increasing attention from commercial breeders.