The foundations of a productive and healthy orchard are the rootstocks that provide anchorage, water and nutrients essential to the above-ground portions of the trees. Utilization of composite trees has increased the efficiency of breeding productive apple trees by dividing the selection of scion traits and rootstock traits into two genetically (and functionally) different specimens, which are then brought together through grafting. As part of the tree, the rootstock influences many factors in addition to tree size, particularly productivity, fruit quality, pest resistance, stress tolerance and ultimately profitability. Understanding how scion properties are modulated by rootstocks allows targeting of traits that may be selected to improve whole tree performance by improving rootstock performance. This chapter examines apple-breeding methods and explores how rootstocks affect scion traits, before addressing the impact of rootstocks on disease and pest resistance.