Genetic improvement of pigs has been achieved by selection of individuals for breeding based on estimated breeding values (EBV), derived using phenotypes for important traits. Ideally, phenotypes on the individual itself and its relatives are utilized in order to obtain the most accurate estimate of the breeding value of the individual. However, there are multiple challenges and limitations associated with these phenotype-based programs. Many of these can be overcome by using molecular information to help predict breeding values and inform selection decisions. This chapter describes how molecular genetic information can be used to enhance selection programs in pigs, what is required to develop such information, and what strategies are available for the use of molecular information in breeding programs. Example cases, challenges and future prospects are also reviewed.