There are currently around ten diseases of sugarcane known to be caused by viruses. In recent years our understanding of these diseases has greatly benefited from access to low-cost sequencing technologies which have revolutionized virus discovery, improved our understanding of genetic variation in viral populations, improved diagnostic options, and helped us to understand gene functions and identify gene targets for control. This chapter will address the broad themes of virus discovery, genetic variation, diagnostic technologies and control. The chapter presents case studies describing the impact of two major viral diseases in Papua New Guinea and Indonesia.