Fusarium wilt is a disease of cotton (Gossypium hirstum) caused by the soil-borne fungal pathogen, Fusarium oxysporum sp vasinfectum (Fov). This disease was first reported in Australia in 1993 in the Darling Downs, and since then it has been steadily spreading to other cotton growing areas. There is currently no effective control for Fov in infected soils; spores can survive in soil for up to 10 years and can be spread over long distances in infected soil. Fusarium wilt is of serious concern to the cotton industry. At present, commercial cotton cultivars range from susceptible to moderately resistant and no completely resistant cultivars are available. Little is known about the interactions between cotton and FOV and it is not clear what factors are involved in the expression of resistance or susceptibility to this disease. New sources of resistance or increased tolerance to this disease are needed urgently by cotton growers. The aim of this study is to investigate cotton's defence responses to FOV infection, and to identify genes whose expression is associated with improved resistance. Plant pathogen interactions are complex and plants will respond to infection with an arsenal of different defences. Plant responses will be reflected in the expression changes of certain plant genes. Gene expression changes due to pathogen attack are thought to be involved in defence against that pathogen. By examining the gene expression changes in cotton plants infected with Fov we hope to discover some of the defence response strategies used by cotton. We have used microarray technology to examine the gene expression changes occurring in infected cotton. The power of this tool is the ability to examine expression changes of thousands of genes simultaneously.