The results of annual disease surveys continue to indicate the importance of soil-borne plant pathogens. Seedling diseases are controlled by the use of fungicide seed treatments. Current and potential seed treatments are being evaluated in annual field experiments. Verticillium wilt has been effectively controlled by the repeated use of resistant cultivars. Black root rot and Fusarium wilt are widespread and particularly significant. Black root rot is found in all cotton production areas but is more important in the cooler areas. The pathogen has been dispersed by the activities of cotton growers. There is no evidence of host plant resistance to black root rot of cotton and current control options are limited to biofumigation with a green manure crop of vetch, summer flooding and delaying the planting time to avoid cool conditions early in the season. The distribution of Fusarium wilt is continuing to increase. The pathogen appears to have originated from native populations of Fusarium oxysporum and resistance to the pathogen has been found in some native Gossypium spp. Slow but significant progress has been made in breeding cotton cultivars with better resistance to the pathogen. Progress has also been made in understanding some of the mechanisms of resistance. Several control options have been, or are being, evaluated and an integrated disease management strategy for Fusarium wilt is being developed. The strategy currently includes delayed incorporation of residues from the previous crop, bare fallow rotation, delayed planting into moisture, use of a cultivar with a high F.rank and use of rolling cultivators to minimise damage to the roots.