Over the last 20 years stone fruit rootstock development has begun shifting from seedling to clonal types, many of interspecific origin. Publicly funded breeding programs have produced most of these rootstocks due to the time, cost, and risk associated with their development; however, private industry is emerging as a significant contributor of many of the newer rootstocks. Particularly noteworthy among recent releases has been the incorporation of resistance to soilborne diseases, nematodes, waterlogging and vigor control, the last most notably in recent cherry rootstocks. Nevertheless, despite the remarkable progress in the development of clonal stocks, seedling rootstocks still dominate most stone fruit industries around the world, if only because of their relatively low cost, ease of propagation, and proven utility. Many opportunities and challenges remain to be addressed in the areas of disease and insect resistance, adaptation to biotic and abiotic stresses, graft compatibility, and rootstock influence on scion performance and fruit quality. Biotechnology is beginning to show potential in accelerating rootstock development. With the development of markers to assist selection for difficult to evaluate traits, new rootstocks with resistance to multiple diseases are feasible. Future prospects for breeding are presented.