Regular disease surveys of commercial crops in all cotton growing areas of New South Wales have monitored the relative importance and distribution of those diseases present. Bacterial blight, which was causing severe losses, has been controlled in susceptible cultivars by the development and implementation of a seed scheme to reduce the level of seed infestation. Blight resistant cultivars have also been released and widely adopted. The increased adoption of reduced tillage practices and the reliance on very susceptible cultivars coupled with conducive weather conditions have resulted in a significant increase in the incidence and importance of verticillium wilt. A cultivar with some resistance to verticillium wilt has just been released. The control of seedling diseases has relied on fungicide seed treatments with very little use of 'hopper-box' or 'in furrow' treatments. Phytophthora boll rot and black root rot have only been reported in Australia in recent years.

Many of the diseases considered important in other cotton growing areas of the world are not present in Australia and the exclusion of these diseases by effective quarantine is important.