Diseases are limiting factors of sugarcane production and breeding for resistance to diseases is a major goal in sugarcane variety improvement. Diseases result from complex interactions between plants, pathogens and environment, including humans and insect vectors of pathogens. History has shown that durability of resistance of sugarcane to diseases varies according to the host cultivar and to the pathogen in a given environment. Some sugarcane cultivars have been grown for decades without losing efficiency of resistance to the disease they were bred or screened for; others became susceptible and showed disease symptoms rapidly after being grown commercially. Disease outbreaks and breakdown or overcoming of plant resistance suggesting changes in the pathogen populations have been observed for several sugarcane diseases. Emergence of new pathogens or new strains of a pathogen generally results in a change of the varieties grown in a sugarcane growing area. Pathogen population genetics must therefore be taken into consideration for breeding and screening new sugarcane varieties for resistance to diseases. Knowing the genetic diversity of a pathogen in a given location is very important, especially when plants are artificially inoculated with pathogens for screening. Furthermore, sugarcane genetics is very complex and few disease specific resistance genes have been identified so far, and selection for these traits is also complex. Sequencing and analysis of genome variation of sugarcane pathogens varying in virulence should result, in the future, in the identification and comprehension of the molecular determinants involved in these genetic changes, and subsequently also facilitate breeding for resistance.