The movement of plant propagation material across countries and continents allows for the exchange of high-quality planting material providing producers with superior germplasm, and enhancing farm sustainability and profits. However, this practice has hidden dangers, including the potential of moving infectious agents to areas where they are not endemic. This chapter takes a systems-based approach on the detection, elimination and safeguarding against systemic pathogens that affect clonally propagated fruit crops. The steps taken to improve propagation material are comprehensively discussed and a number of case studies are presented including blackberry yellow vein disease and raspberry crumbly fruit and decline. New technologies that allow for the rapid and accurate characterization of plant pathogens are discussed. These include tools such as high throughput sequencing which has proved invaluable in assessing the health status of high value plants and for the rapid identification and characterization of unknown viruses.