Plant diseases are currently threatening the productivity and sustainability of the cotton industry. Regular disease surveys in NSW have enabled accurate observation of the changing distribution and severity of diseases over time. The relative risks are low for bon rots, Alternaria leaf spot and bacterial blight, medium for seedling disease and Verticillium wilt, and high for black rootrot and fusarium wilt. Issues that need to be addressed include regional differences, potential new threats, and the complexity of pathosystems (pathogens x hosts x fields x regions). Research should include (1) continued investigation of factors contributing to the spread and severity of diseases and (ii) further development and evaluation of tools for integrated disease management.