For more than two millennia, superior fruit tree genotypes have been grafted onto rootstocks to maintain the genetic identity of the desirable scions. Until the 20th century most fruit trees were grafted onto seedling rootstocks. Following the classification, evaluation, and propagation of clonal rootstocks during the early 1900s, dwarfing rootstocks became important to the commercial apple industries. Although trees on dwarfing rootstocks are more economical to maintain, and are more precocious and productive than trees on seedling rootstocks, there remains a need for dwarfing rootstocks to be adapted to different growing conditions. During the past 100 years, considerable effort has been made to understand the physiological changes in the scion induced by rootstocks. More recently, molecular techniques have been utilized to identify the genes that control interactions between scion and rootstock. Modern rootstock breeding programs are combining molecular and traditional techniques to develop rootstocks that are dwarfing, productive, and tolerant to biotic and abiotic stresses. In this chapter, the history, development and current use of apple rootstocks, the current understanding of rootstock–scion interactions, and current efforts to develop and evaluate superior rootstocks are discussed.